← Back to search
9gkm

Structure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains

Method: ELECTRON MICROSCOPY Dmax: 131.4 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–75 Chain C； UniProt 1–76 Mutation：K29C Polyubiquitin-B × 1 （P0CG47） Isoform 3 of E3 ubiquitin-protein ligase TRIP12 × 1 （Q14669） SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.69 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9GKM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11SY Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused) Deposited 2026-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM HEPES, pH 7.6, 150 mM KCl, 5 mM MgCl2, 2 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
1OGW Synthetic Ubiquitin with fluoro-Leu at 50 and 67 Deposited 2003-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：RESIDUES 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；SEEDED FROM DROP CONTAINING CONTAINING 5 MUL 20MG/ML UBIQUITIN AND 5 MUL 30% PEG 4000 IN 50MM CACODYLATE-HCL PH 5.6. STORED IN 38% PEG 4000.
Resolution 1.32 Å
2L3Z Proton-Detected 4D DREAM Solid-State NMR Structure of Ubiquitin Deposited 2010-09-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP Residues 1-76
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 4.1；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 100 % [U-13C; U-15N; U-2H] Ubiquitin, 20% H2O, 80% D2O in crystallization buffer | 20% H2O, 80% D2O in crystallization buffer
Resolution not provided
2LD9 Backbone Structure of Ubiquitin determined using Backbone amide NOEs and Backbone N-H and N-C RDCs Deposited 2011-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 76–152（77 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR sample composition 1 mM [U-99% 13C; U-99% 15N] sodium phosphate-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LVO Structure of the gp78CUE domain bound to monubiquitin Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Pressure ambient
NMR sample composition 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LVP gp78CUE domain bound to the distal ubiquitin of K48-linked diubiquitin Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Pressure ambient
NMR sample composition 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LVQ gp78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Pressure ambient
NMR sample composition 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LZ6 Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.2 mM [U-99% 15N] CD2AP SH3-C, 1 mM Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-99% 15N] Ubiquitin, 1 mM CD2AP SH3-C, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 0.46 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.828 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.37 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.78 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MBO K11-linked Diubiquitin average solution structure at pH 6.8, 0 mM NaCl Deposited 2013-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Pressure ambient
NMR sample composition 75 uM [U-99% 15N] ubiquitin, 20 mM sodium phosphate, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2MBQ K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl Deposited 2013-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 75 uM [U-99% 15N] ubiquitin, 20 mM sodium phosphate, 150 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2MCN Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications Deposited 2013-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.2 mM [U-99% 15N] CD2AP SH3-A, 1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-99% 15N] ubiquitin, mM CD2AP SH3-A, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 0.46 mM [U-99% 15N ubiquitin | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.37 mM [U-99% 15N] ubiquitin | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.75 mM [U-99% 15N] ubiquitin | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-A, 1.75 MM [U-99% 15N] ubiquitin | 90% H2O/10% D2O
Resolution not provided
2MI8 Solution structure of lysine-free (K0) ubiquitin Deposited 2013-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：K6R, K11R, K27R, K29R, K33R, K48R, K63R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 5 % [U-2H] D2O, 50 mM TRIS, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MJ5 Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin Deposited 2013-12-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residuses 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Pressure ambient
NMR sample composition 20 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95 % H2O-8, 5 % D2O-9, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium phosphate-10, 5 mM potassium chloride-11, 1 mM EDTA-12, 1 mM benzamidine-13, 1 mM DTT-14, 0.02 % sodium azide-15, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-16, 12.5 mg/mL Pf1 phage-17, 150 mM sodium chloride-18, 95 % H2O-19, 5 % D2O-20, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-21, 2 mM Ubiquitin-22, 12.5 mg/mL Pf1 phage-23, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium phosphate-24, 5 mM potassium chloride-25, 1 mM EDTA-26, 1 mM benzamidine-27, 1 mM DTT-28, 0.02 % sodium azide-29, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-30, 12.5 mg/mL Pf1 phage-31, 150 mM sodium chloride-32, 95 % H2O-33, 5 % D2O-34, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-35, 2 mM Ubiquitin-36, 12.5 mg/mL Pf1 phage-37, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2 mM NBR1_UBA-38, 0.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-39, 12.5 mg/mL Pf1 phage-40, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-100% 15N] NBR1_UBA-41, 4.5 mM Ubiquitin-42, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MOR A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings Deposited 2014-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；292 K；Pressure ambient
NMR measurement conditions pH 6.6；298 K；Pressure ambient
NMR measurement conditions pH 6.6；304 K；Pressure ambient
NMR sample composition 0.7 mM [U-13C; U-15N] Ubiquitin, 10 mM phosphate, 5 w/v DMPC:DHPC(3:1), 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2MRE NMR structure of the Rad18-UBZ/ubiquitin complex Deposited 2014-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient
NMR sample composition 0.5 mM [U-13C; U-15N] Ubiquitin-binding zinc finger (UBZ) domain from human Rad18, 5 mM Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mM [U-13C; U-15N] Ubiquitin, 7-10 mM Ubiquitin-binding zinc finger (UBZ) domain from human Rad18, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MWS Structure of the complex of ubiquitin and the ubiquitin-like (UBL) domain of Ddi1 Deposited 2014-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：T12(3X9) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 0.002；Pressure ambient
NMR sample composition 250 uM chain A, 250 uM [U-100% 15N] chain B, 5 % D2O, 20 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N2K Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand Deposited 2015-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–71（71 aa）
Mutation：N25C, K48C MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 2 SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 0.5 mM [U-100% 15N] N25C_MTS protein-1, 10 % v/v [U-99% 2H] D2O-2, 100 mM sodium chloride-3, 10 mM sodium acetate-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 15N] K48C_MTS protein-5, 10 % v/v [U-99% 2H] D2O-6, 100 mM sodium chloride-7, 10 mM sodium acetate-8, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] N25C_MTS mixture protein-9, 10 % v/v [U-99% 2H] D2O-10, 100 mM sodium chloride-11, 10 mM sodium acetate-12, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] K48C_MTS mixture protein-13, 10 % v/v [U-99% 2H] D2O-14, 100 mM sodium chloride-15, 10 mM sodium acetate-16, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 15N] 15N_distal-14N_proximal-17, 10 % v/v [U-99% 2H] D2O-18, 100 mM sodium chloride-19, 10 mM sodium acetate-20, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 15N] 14N_distal-15N_proximal-21, 10 % v/v [U-99% 2H] D2O-22, 100 mM sodium chloride-23, 10 mM sodium acetate-24, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RR9 The solution structure of the K63-Ub2:tUIMs complex Deposited 2010-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；310 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 2.4 mM ubiquitin 1-1, 2.4 mM ubiquitin 2-2, 2.4 mM [U-13C; U-15N] tandem UIMs of Rap80-3, 1 mM DTT-4, 50 mM sodium phosphate-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mM ubiquitin 1-6, 2 mM ubiquitin 2-7, 2 mM [U-13C; U-15N; U-70% 2H] tandem UIMs of Rap80-8, 1 mM DTT-9, 50 mM sodium phosphate-10, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2.9 mM [U-13C; U-15N] ubiquitin 1-11, 2.9 mM ubiquitin 2-12, 2.9 mM tandem UIMs of Rap80-13, 1 mM DTT-14, 50 mM sodium phosphate-15, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2.9 mM ubiquitin 1-16, 2.9 mM [U-13C; U-15N] ubiquitin 2-17, 2.9 mM tandem UIMs of Rap80-18, 1 mM DTT-19, 50 mM sodium phosphate-20, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RSU Alternative structure of Ubiquitin Deposited 2012-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：Q41N No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.5 mM [U-15N] protein-1, 20 mM [U-99% 2H] TRIS-2, 1 mM DSS-3, 250 mM sodium chloride-4, 6 mg/mL Pf1 bacteriopharge-5, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 2.0 mM [U-99% 13C; U-99% 15N] protein-6, 20 mM [U-99% 2H] TRIS-7, 1 mM DSS-8, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2RU6 The pure alternative state of ubiquitin Deposited 2013-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：Q41N No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 20；Pressure 250
NMR sample composition 20 mM [U-100% 2H] Tris(hydroxymethyl)aminomethane-1, 2 mM [U-100% 13C; U-100% 15N] ubiquitin-2, 0.2 mM DSS-3, 88% H2O/12% D2O | 88% H2O/12% D2O
Resolution not provided
3ALB Cyclic Lys48-linked tetraubiquitin Deposited 2010-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；289 K；20% PEG 3350, 0.2M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.85 Å R-free 0.239
3AUL Crystal structure of wild-type Lys48-linked diubiquitin in an open conformation Deposited 2011-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 77–152（76 aa） Fragment：Ubiquitin
Chain B 77–152（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20% PEG 3350, 0.2M litium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.39 Å R-free 0.252
3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–152（152 aa） Fragment：linear di ubiquitin, UNP residues 1-152
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.211
3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–152（152 aa） Fragment：linear di ubiquitin, UNP residues 1-152
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.211
3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–152（152 aa） Fragment：linear di ubiquitin, UNP residues 1-152
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.211
3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–152（152 aa） Fragment：linear di ubiquitin, UNP residues 1-152
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.211
3B0A Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–152（152 aa） Fragment：linear di ubiquitin, UNP residues 1-152
Not recorded TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.45M tri-ammonium citrate (pH 7.0), 3% 1,6-diaminohexane, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K
Resolution 1.90 Å R-free 0.227
3B0A Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–152（152 aa） Fragment：linear di ubiquitin, UNP residues 1-152
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.45M tri-ammonium citrate (pH 7.0), 3% 1,6-diaminohexane, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K
Resolution 1.90 Å R-free 0.227
3OFI Crystal structure of human insulin-degrading enzyme in complex with ubiquitin Deposited 2010-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；10-13% PEG MME 5000, 100 MM HEPES PH 7.0. 4-14% Tacsimate, 10% Dioxane, vapor diffusion, hanging drop, temperature 291K
Resolution 2.35 Å R-free 0.240
3OFI Crystal structure of human insulin-degrading enzyme in complex with ubiquitin Deposited 2010-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；10-13% PEG MME 5000, 100 MM HEPES PH 7.0. 4-14% Tacsimate, 10% Dioxane, vapor diffusion, hanging drop, temperature 291K
Resolution 2.35 Å R-free 0.240
3Q3F Engineering Domain-Swapped Binding Interfaces by Mutually Exclusive Folding: Insertion of Ubiquitin into position 103 of Barnase Deposited 2010-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–76（75 aa） Fragment：UNP P00648 48-150 and 151-157, UNP P0CG48 residues 2-76
Not recorded SO4 SULFATE ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10 mM Tris (pH 8.0), 1 M (NH4)2SO4, 1.5% isopropanol (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.17 Å R-free 0.233
3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) TLA L(+)-TARTARIC ACID × 2 N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.277
3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) TLA L(+)-TARTARIC ACID × 2 CL CHLORIDE ION × 1 N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.277
3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.277
3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.277
3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin-like 1
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.91 Å R-free 0.227
3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin-like 1
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.91 Å R-free 0.227
3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa） Fragment：Ubiquitin-like 1
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.91 Å R-free 0.227
3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa） Fragment：Ubiquitin-like 1
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.91 Å R-free 0.227
3U30 Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin Deposited 2011-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–169（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；18% isopropanol, 0.09 M MES, 19.8% PEG 2K MME, 10 mM sodium bromide., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.43 Å R-free 0.258
3U30 Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin Deposited 2011-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 18–169（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；18% isopropanol, 0.09 M MES, 19.8% PEG 2K MME, 10 mM sodium bromide., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.43 Å R-free 0.258
3UGB UbcH5c~Ubiquitin Conjugate Deposited 2011-11-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa） Fragment：unp residues 1-76
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.252
3V6C Crystal Structure of USP2 in complex with mutated ubiquitin Deposited 2011-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 74–150（77 aa）
Mutation：G76S, K82N, K87T, T88H CL CHLORIDE ION × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；21% PEG 3350,0.2 M CaCl, 0.1 Bis-Tris pH 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.220
3V6E Crystal Structure of USP2 and a mutant form of Ubiquitin Deposited 2011-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 74–150（77 aa）
Mutation：G76S, K82N, T85S, T88H ZN ZINC ION × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；21% PEG3350, 0.2 M Calcium Chloride,0.1 Bis-Tris pH 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.234
3VFK The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier Deposited 2012-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GCS 2-amino-2-deoxy-beta-D-glucopyranose × 1 T55 8-METHYLNONANOIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.1 M magnesium chloride, 0.1 M sodium acetate 4.6, 18% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.306
3VUW Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Resolution 1.95 Å R-free 0.222
3VUW Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Resolution 1.95 Å R-free 0.222
3VUW Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Resolution 1.95 Å R-free 0.222
3VUX Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Ubiquitin
Not recorded EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.203
3VUX Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.203
3VUX Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.203
3VUY Crystal structure of A20 ZF7 in complex with linear tetraubiquitin Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Resolution 1.98 Å R-free 0.255
3VUY Crystal structure of A20 ZF7 in complex with linear tetraubiquitin Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Resolution 1.98 Å R-free 0.255
3VUY Crystal structure of A20 ZF7 in complex with linear tetraubiquitin Deposited 2012-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Resolution 1.98 Å R-free 0.255
3WXE Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin Deposited 2014-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–148（148 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50mM Tris-HCl buffer, 9% PEG4000, 100mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.50 Å R-free 0.247
3WXF Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin Deposited 2014-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–148（148 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl buffer, 23% PEG3350, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.229
3WXF Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin Deposited 2014-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–148（148 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl buffer, 23% PEG3350, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.229
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Resolution 2.21 Å R-free 0.211
4AUQ Structure of BIRC7-UbcH5b-Ub complex. Deposited 2012-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa） Fragment：UBIQUITIN, RESIDUES 1-76
Chain F 1–76（76 aa） Fragment：UBIQUITIN, RESIDUES 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.18 Å R-free 0.249
4BOS Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa） Fragment：RESIDUES 1-76
Chain E 1–76（76 aa） Fragment：RESIDUES 1-76
Not recorded NO3 NITRATE ION × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 21% PEG 3,350, 100 MM SODIUM ACETATE, 200 MM MAGNESIUM NITRATE, PH 5.6
Resolution 2.35 Å R-free 0.238
4BOZ Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5
Resolution 3.03 Å R-free 0.254
4BOZ Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5
Resolution 3.03 Å R-free 0.254
4BOZ Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5
Resolution 3.03 Å R-free 0.254
4BVU Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate Deposited 2013-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M TRIS PH 8.5, 20% ETOH
Resolution 2.70 Å R-free 0.291
4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.30 Å R-free 0.280
4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain M 1–76（76 aa）
Chain N 1–76（76 aa）
Chain O 1–76（76 aa）
Chain P 1–76（76 aa）
Chain Q 1–76（76 aa）
Chain R 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.30 Å R-free 0.280
4DDI Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；25% PEG1500, 0.1 M SPG, pH 8.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.80 Å R-free 0.273
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
4DHZ The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub Deposited 2012-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；21% PEG10000, 0.1 M sodium chloride, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.11 Å R-free 0.288
4DHZ The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub Deposited 2012-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；21% PEG10000, 0.1 M sodium chloride, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.11 Å R-free 0.288
4FJV Crystal Structure of Human Otubain2 and Ubiquitin Complex Deposited 2012-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；279 K；15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Resolution 2.05 Å R-free 0.267
4FJV Crystal Structure of Human Otubain2 and Ubiquitin Complex Deposited 2012-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；279 K；15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Resolution 2.05 Å R-free 0.267
4FJV Crystal Structure of Human Otubain2 and Ubiquitin Complex Deposited 2012-06-12 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 6 NEH ETHANAMINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；279 K；15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Resolution 2.05 Å R-free 0.267
4HK2 U7Ub25.2540 Deposited 2012-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–150（76 aa）
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
Resolution 1.40 Å R-free 0.236
4HK2 U7Ub25.2540 Deposited 2012-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 75–150（76 aa）
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
Resolution 1.40 Å R-free 0.236
4HK2 U7Ub25.2540 Deposited 2012-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 75–150（76 aa）
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
Resolution 1.40 Å R-free 0.236
4HK2 U7Ub25.2540 Deposited 2012-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 75–150（76 aa）
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
Resolution 1.40 Å R-free 0.236
4HXD Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases Deposited 2012-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–75（75 aa）
Not recorded 4LJ 1.7.6 3-bromanylpropan-1-amine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.25 M LiSO4, 0.10 M Bis-Tris, 29% PEG 3350, 40% (v/v) 1,3-butanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.85 Å R-free 0.278
4HXD Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases Deposited 2012-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded 4LJ 1.7.6 3-bromanylpropan-1-amine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.25 M LiSO4, 0.10 M Bis-Tris, 29% PEG 3350, 40% (v/v) 1,3-butanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.85 Å R-free 0.278
4I6L Crystal structure of OTUB1 in complex with ubiquitin variant Deposited 2012-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–150（74 aa） Fragment：UNP residues 77-150
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, and 20% (w/v) PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.49 Å R-free 0.266
4I6N Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester Deposited 2012-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 NA SODIUM ION × 1 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；3M ammonium sulfate, 0.1M bicine, 2mM L-glutathione, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.70 Å R-free 0.211
4I6N Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester Deposited 2012-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；3M ammonium sulfate, 0.1M bicine, 2mM L-glutathione, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.70 Å R-free 0.211
4IG7 Crystal structure of Trichinella spiralis UCH37 bound to Ubiquitin vinyl methyl ester Deposited 2012-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.2 M ammonium chloride, 18% PEG3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.239
4IUM Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin Deposited 2013-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa） Fragment：UNP residues 1-75
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；100 mM MES, pH 6.2, 18% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.45 Å R-free 0.178
4JQW Crystal Structure of a Complex of NOD1 CARD and Ubiquitin Deposited 2013-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；291 K；100mM PCB, 25% PEG1500, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.270
4K1R Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin Deposited 2013-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 75–152（78 aa）
Not recorded ZN ZINC ION × 3 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.63 Å R-free 0.215
4K1R Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin Deposited 2013-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 75–152（78 aa）
Not recorded ZN ZINC ION × 3 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.63 Å R-free 0.215
4K1R Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin Deposited 2013-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 75–152（78 aa）
Chain D 75–152（78 aa）
Not recorded ZN ZINC ION × 6 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.63 Å R-free 0.215
4K7S Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-73
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.271
4K7S Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-73
Not recorded ZN ZINC ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.271
4K7S Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-73
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.271
4K7U Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 4 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.196
4K7U Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 3 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.196
4K7U Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.196
4K7W Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 4 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.267
4K7W Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.267
4K7W Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 3 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.267
4KSK Gumby/Fam105B in complex with ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 76–152（77 aa） Fragment：unp residues 76-152
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.268
4KSK Gumby/Fam105B in complex with ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 76–152（77 aa） Fragment：unp residues 76-152
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.268
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 76–228（153 aa） Fragment：linear diubiquitin (unp residues 76-228)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.83 Å R-free 0.254
4LCD Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 Deposited 2013-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–75（75 aa） Fragment：UNP residues 1-75
Mutation：G75C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；298 K；0.1M Bis Tris Propane, 21% w/v PEG3350, 1% w/v polypropylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.299
4LCD Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 Deposited 2013-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa） Fragment：UNP residues 1-75
Mutation：G75C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；298 K；0.1M Bis Tris Propane, 21% w/v PEG3350, 1% w/v polypropylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.299
4LDT The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub Deposited 2013-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 4 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well solution + 10% ethylene glycol, flash frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 1.90 Å R-free 0.223
4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 76–152（77 aa） Fragment：UNP residues 76-152
Not recorded U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.259
4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 76–152（77 aa） Fragment：UNP residues 76-152
Not recorded U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.259
4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 76–152（77 aa） Fragment：UNP residues 76-152
Not recorded U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.259
4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 76–152（77 aa） Fragment：UNP residues 76-152
Not recorded U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.259
4MM3 Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin aldehyde Deposited 2013-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES, pH 7.5, 10% isopropanol, 20% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.75 Å R-free 0.279
4MSM Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin Deposited 2013-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：UNP residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2M Ammonium Phosphate dibasic, 20%w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.74 Å R-free 0.225
4MSM Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin Deposited 2013-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–152（76 aa） Fragment：UNP residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 6 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2M Ammonium Phosphate dibasic, 20%w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.74 Å R-free 0.225
4MSQ Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin Deposited 2013-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：UNP residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；0.2 M Sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.95 Å R-free 0.207
4MSQ Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin Deposited 2013-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–152（76 aa） Fragment：UNP residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 6 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；0.2 M Sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.95 Å R-free 0.207
4NQK Structure of an Ubiquitin complex Deposited 2013-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 76–152（77 aa） Fragment：UNP residues 76-152
Chain F 76–152（77 aa） Fragment：UNP residues 76-152
Chain G 76–152（77 aa） Fragment：UNP residues 76-152
Chain H 76–152（77 aa） Fragment：UNP residues 76-152
Chain I 76–152（77 aa） Fragment：UNP residues 76-152
Chain J 76–152（77 aa） Fragment：UNP residues 76-152
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22% PEG3350, 0.2 M Tri-Li Citrate, 3% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.70 Å R-free 0.285
4UN2 Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin Deposited 2014-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000
Resolution 1.51 Å R-free 0.196
4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE
Resolution 2.04 Å R-free 0.223
4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE
Resolution 2.04 Å R-free 0.223
4V3L RNF38-UB-UbcH5B-Ub complex Deposited 2014-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa） Fragment：RESIDUES 77-152
Chain D 77–152（76 aa） Fragment：RESIDUES 77-152
Not recorded EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 50 MM HEPES, PH 7.5, 0.2 M MAGNESIUM ACETATE AND 13% (W/V) PEG 8K
Resolution 1.53 Å R-free 0.193
4XOK Observing the overall rocking motion of a protein in a crystal. Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0, 35% PEG 1500, 25mM Zn Acetate
Resolution 2.20 Å R-free 0.324
4XOK Observing the overall rocking motion of a protein in a crystal. Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0, 35% PEG 1500, 25mM Zn Acetate
Resolution 2.20 Å R-free 0.324
4XOK Observing the overall rocking motion of a protein in a crystal. Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0, 35% PEG 1500, 25mM Zn Acetate
Resolution 2.20 Å R-free 0.324
4XOL Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals. Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.33；293 K；100mM MES pH 6.33, 20% PEG 3350, 100mM Zn Acetate.
Resolution 2.91 Å R-free 0.269
4XOL Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals. Deposited 2015-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.33；293 K；100mM MES pH 6.33, 20% PEG 3350, 100mM Zn Acetate.
Resolution 2.91 Å R-free 0.269
4ZQS New compact conformation of linear Ub2 structure Deposited 2015-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–152（152 aa）
Chain B 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1M Tris-HCl pH 8.0, 0.1M magnesium acetate, 20% PEG 3350, 20% PEG 400
Resolution 1.80 Å R-free 0.232
5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 9.50 Å
5AIU A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain F 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions 1,2-ETHANEDIOL
Resolution 2.21 Å R-free 0.255
5B83 Crystal structure of Optineurin UBAN in complex with linear ubiquitin Deposited 2016-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–304（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16% PEG 3350, 250mM Potassium formate
Resolution 2.69 Å R-free 0.254
5B83 Crystal structure of Optineurin UBAN in complex with linear ubiquitin Deposited 2016-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–304（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16% PEG 3350, 250mM Potassium formate
Resolution 2.69 Å R-free 0.254
5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–74（74 aa） Fragment：UNP residues 1-74
Mutation：T9A, K11W, T12G, Q62R, K63Y, E64D, T66Q, L71G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization. Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04. Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
Resolution 3.00 Å R-free 0.277
5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–74（74 aa） Fragment：UNP residues 1-74
Mutation：T9A, K11W, T12G, Q62R, K63Y, E64D, T66Q, L71G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization. Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04. Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
Resolution 3.00 Å R-free 0.277
5C7M CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT Deposited 2015-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa） Fragment：UNP residues 1-75
Mutation：Q2H, F3L, T9R, I44L, A46G, K48N, Q49K, T66N, H68Y, V70L, L73R, R74L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml. The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant
Resolution 3.03 Å R-free 0.297
5C7M CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT Deposited 2015-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–75（75 aa） Fragment：UNP residues 1-75
Mutation：Q2H, F3L, T9R, I44L, A46G, K48N, Q49K, T66N, H68Y, V70L, L73R, R74L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml. The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant
Resolution 3.03 Å R-free 0.297
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa）
Mutation：K48LYQ, G76AYE Non-standard monomer：Yes (specific site not provided by mmCIF) ACT ACETATE ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–75（75 aa）
Mutation：K48LYQ, G76AYE Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5H07 TNIP2-Ub complex, C2 form Deposited 2016-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–228（228 aa） Fragment：UNP residues 1-228
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；ammonium acetate, PEG3350, Tris-HCl
Resolution 2.59 Å R-free 0.273
5NL4 Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 35 mM Zn(CH3COO)2
Resolution 1.32 Å R-free 0.213
5NL4 Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 35 mM Zn(CH3COO)2
Resolution 1.32 Å R-free 0.213
5NL4 Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 35 mM Zn(CH3COO)2
Resolution 1.32 Å R-free 0.213
5NLF Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 6 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 100 mM Zn(CH3COO)2
Resolution 1.50 Å R-free 0.180
5NLF Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 100 mM Zn(CH3COO)2
Resolution 1.50 Å R-free 0.180
5NLF Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 100 mM Zn(CH3COO)2
Resolution 1.50 Å R-free 0.180
5NLI Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 4 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 35 mM Zn(CH3COO)2 and 10% v/v TFE
Resolution 1.53 Å R-free 0.202
5NLI Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 ETF TRIFLUOROETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 35 mM Zn(CH3COO)2 and 10% v/v TFE
Resolution 1.53 Å R-free 0.202
5NLI Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 35 mM Zn(CH3COO)2 and 10% v/v TFE
Resolution 1.53 Å R-free 0.202
5NMC Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb Deposited 2017-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded ACT ACETATE ION × 2 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2 and 20% v/v TFE
Resolution 1.70 Å R-free 0.276
5NMC Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb Deposited 2017-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded ACT ACETATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2 and 20% v/v TFE
Resolution 1.70 Å R-free 0.276
5NMC Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb Deposited 2017-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Not recorded ACT ACETATE ION × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2 and 20% v/v TFE
Resolution 1.70 Å R-free 0.276
5OE7 Structure of OTULIN bound to the Met1-linked diubiquitin activity probe Deposited 2017-07-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–146（146 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；1.9-2.1 M Ammonium sulphate, 100 mM bis-tris
Resolution 2.95 Å R-free 0.309
5OHM K33-specific affimer bound to K33 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 609–684（76 aa）
Chain C 609–684（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% PEG3350 0.2M potassium thiocyanate
Resolution 3.80 Å R-free 0.282
5OHM K33-specific affimer bound to K33 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 609–684（76 aa）
Chain G 609–684（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% PEG3350 0.2M potassium thiocyanate
Resolution 3.80 Å R-free 0.282
5OHM K33-specific affimer bound to K33 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 609–684（76 aa）
Chain K 609–684（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% PEG3350 0.2M potassium thiocyanate
Resolution 3.80 Å R-free 0.282
5OHV K33-specific affimer bound to K33 diUb Deposited 2017-07-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；295 K；21% PEG 3350 200 mM Li2SO4 100 mM NaOAc pH 5.2
Resolution 2.80 Å R-free 0.224
5OXH C-terminally retracted ubiquitin T66V/L67N mutant Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：T66V, L67N Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；3.2 M ammonium sulfate, 0.1 M bicine (pH 9.0); 1:1 protein to reservoir ratio
Resolution 1.60 Å R-free 0.223
5OXI C-terminally retracted ubiquitin L67S mutant Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：L67S SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；3 M ammonium sulfate, 0.1 M MES (pH 6.0); 2:1 protein to reservoir ratio
Resolution 1.63 Å R-free 0.237
5OXI C-terminally retracted ubiquitin L67S mutant Deposited 2017-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：L67S SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；3 M ammonium sulfate, 0.1 M MES (pH 6.0); 2:1 protein to reservoir ratio
Resolution 1.63 Å R-free 0.237
5WQ4 Crystal structure of OPTN and linear diubiquitin complex Deposited 2016-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289.15 K；30% w/v PEG 3350, 0.1 M HEPES (pH 7.5)
Resolution 3.00 Å R-free 0.303
5WQ4 Crystal structure of OPTN and linear diubiquitin complex Deposited 2016-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289.15 K；30% w/v PEG 3350, 0.1 M HEPES (pH 7.5)
Resolution 3.00 Å R-free 0.303
5ZQ3 PDE-Ubiquitin Deposited 2018-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 10000, Bicine
Resolution 2.18 Å R-free 0.213
5ZQ3 PDE-Ubiquitin Deposited 2018-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 10000, Bicine
Resolution 2.18 Å R-free 0.213
5ZQ4 PDE-Ubi-ADPr Deposited 2018-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 10000, Bicine
Resolution 2.22 Å R-free 0.226
5ZQ4 PDE-Ubi-ADPr Deposited 2018-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 10000, Bicine
Resolution 2.22 Å R-free 0.226
5ZQ5 SidE-Ubi Deposited 2018-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：R42A Mutation：R42A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Tacsimate
Resolution 2.49 Å R-free 0.233
5ZQ6 SidE-Ubi-ADPr Deposited 2018-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：R42A Mutation：R42A ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Tacsimate
Resolution 3.01 Å R-free 0.232
5ZQ7 SidE-Ubi-NAD Deposited 2018-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：R42A Mutation：R42A NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Tacsimate
Resolution 2.85 Å R-free 0.239
6A43 R1EN(5-225)-ubiquitin fusion Deposited 2018-06-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E44A, A73C ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；2.0M sodium acetate, 10mM ammonium sulfate, 1% Jeffamine M600
Resolution 2.40 Å R-free 0.241
6A44 R1EN(5-227)-ubiquitin fusion Deposited 2018-06-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–152（76 aa）
Mutation：E44A, A73C ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；283 K；2.0 M sodium acetate, 10 mM ammonium sulfate, 1% Jeffamine M600
Resolution 2.40 Å R-free 0.237
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate
Resolution 2.10 Å R-free 0.249
6B7M Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin Deposited 2017-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；200 mM NaCl, 100 mM Imidazole pH 7.0, 24% PEG 8000
Resolution 1.70 Å R-free 0.196
6B7O Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin Deposited 2017-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM Na Cacodylate pH 7.0, 21% PEG 8000
Resolution 1.85 Å R-free 0.201
6EQI Structure of PINK1 bound to ubiquitin Deposited 2017-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Mutation：T66V L67N GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；The PhPINK1-Nb696-Ub TVLN complex was crystallised at 7 mg/ml using sitting-drop vapour diffusion against 1.3 M Ammonium Tartrate Dibasic, 0.1 M BIS-TRIS Propane pH 7.0 from a 1:1 protein to mother liquor ratio, in 100 nl drops at 295.15 K. Crystals were optimised using streak seeding with a cat whisker at 8.9 mg/ml complex concentration in 1.4 M Ammonium Tartrate, 0.1 M BIS-TRIS Propane pH 6.3 at 295.15 K.
Resolution 3.10 Å R-free 0.234
6K2U Crystal structure of Thr66 ADP-ribosylated ubiquitin Deposited 2019-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1M MMT (Malic Acid, MES and TRIS (1:2:2 Molar Ratio), pH 5.5 adjusted with HCl), 0.1M magnesium chloride, 0.1M zinc acetate 12% PEG8000
Resolution 2.55 Å R-free 0.247
6KBE Structure of Deubiquitinase Deposited 2019-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–152（152 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.34 Å R-free 0.256
6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6N6R Crystal structure of ABIN-1 UBAN in complex with two M1-linked di-ubiquitins Deposited 2018-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 76–228（153 aa）
Chain C 76–228（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30% v/v PEG-MME550, 0.1 M bis-tris pH 6.5, and 0.05 M calcium chloride dihydrate
Resolution 1.95 Å R-free 0.278
6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 3.54 Å
6NXK Ubiquitin binding variants Deposited 2019-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M HEPES pH 7.7, 27.5% PEG3350, 2.5mM APC2 WHB (735-C) + 2.08mM Ubiquitin protein co-mixed
Resolution 2.20 Å R-free 0.266
6NXK Ubiquitin binding variants Deposited 2019-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M HEPES pH 7.7, 27.5% PEG3350, 2.5mM APC2 WHB (735-C) + 2.08mM Ubiquitin protein co-mixed
Resolution 2.20 Å R-free 0.266
6OI4 RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex Deposited 2019-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.76 Å R-free 0.207
6OI4 RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex Deposited 2019-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.76 Å R-free 0.207
6P5B Crystal Structure of MavC in Complex with Ub-UbE2N Deposited 2019-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.2 M Na Malonate, 25% PEG 3350, 10 mM NiCl2
Resolution 2.10 Å R-free 0.232
6Q00 TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1 Deposited 2019-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；10 mM Tris, 200 mM Potassium Formate, 14% (w/v) PEG 3350
Resolution 0.85 Å R-free 0.112
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded K POTASSIUM ION × 2 BR BROMIDE ION × 3 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–76（76 aa）
Not recorded K POTASSIUM ION × 3 BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6RYA Structure of Dup1 mutant H67A:Ubiquitin complex Deposited 2019-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride
Resolution 2.21 Å R-free 0.289
6RYA Structure of Dup1 mutant H67A:Ubiquitin complex Deposited 2019-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride
Resolution 2.21 Å R-free 0.289
6RYA Structure of Dup1 mutant H67A:Ubiquitin complex Deposited 2019-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride
Resolution 2.21 Å R-free 0.289
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.
Resolution 2.80 Å R-free 0.249
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain J 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.
Resolution 2.80 Å R-free 0.249
6SQR Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub Deposited 2019-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–76（76 aa）
Not recorded EDO 1,2-ETHANEDIOL × 12 ZN ZINC ION × 8 NO3 NITRATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；292 K；0.1 M Tris-HCl, pH 8.5, 20% (v/v) PEG Smear High
Resolution 2.18 Å R-free 0.227
6T7F RCR E3 ligase E2-Ubiquitin transthiolation intermediate Deposited 2019-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–73（73 aa）
Not recorded ZN ZINC ION × 6 LWZ 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0
Resolution 2.58 Å R-free 0.256
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 1–76（76 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.60 Å
6TNF Structure of monoubiquitinated FANCD2 in complex with FANCI and DNA Deposited 2019-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM HEPES, 100 mM imidazole, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–76（76 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
6TUV Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin Deposited 2020-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400
Resolution 2.16 Å R-free 0.249
6TUV Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin Deposited 2020-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400
Resolution 2.16 Å R-free 0.249
6TXB Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded NA SODIUM ION × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2 M Sodium malonate, 20% PEG 3350
Resolution 2.18 Å R-free 0.246
6TXB Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2 M Sodium malonate, 20% PEG 3350
Resolution 2.18 Å R-free 0.246
6ULH Structure of MavC in complex with its substrate in R3 spacegroup Deposited 2019-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；0.1 M Sodium Acetate: HCl, pH 4.6 3.5 M Sodium Formate
Resolution 1.97 Å R-free 0.227
6UMP Crystal structure of MavC in complex with substrate mimic in P65 space group Deposited 2019-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium formate, 20% w/v Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.304
6UMS Crystal structure of MavC in complex with its substrate mimic in C222(1) space group Deposited 2019-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.15 M Potassium bromide, 30% (w/v) PEG 2000 MME
Resolution 2.34 Å R-free 0.250
6V5D EROS3 RDC and NOE Derived Ubiquitin Ensemble Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6VAE Mono-ubiquitinated Fanconi Anemia ID complex bound to ICL DNA Deposited 2019-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6VAF Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA Deposited 2019-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain K 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 5 3.5 sec blot time
Resolution 3.37 Å
6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 2 IOD IODIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350, 200-400 mM NaI
Resolution 3.19 Å R-free 0.281
6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 2 IOD IODIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350, 200-400 mM NaI
Resolution 3.19 Å R-free 0.281
6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Not recorded ZN ZINC ION × 2 IOD IODIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350, 200-400 mM NaI
Resolution 3.19 Å R-free 0.281
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain W 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain O 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain U 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
Resolution 1.82 Å R-free 0.208
6W9S Crystal structure of an OTU deubiquitinase from Escherichia albertii bound to ubiquitin Deposited 2020-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.8 M sodium formate, 10% PEG 8K, 10% PEG 1K, 0.1 M sodium acetate pH 4.5
Resolution 2.10 Å R-free 0.253
6WJD SA-like state of human 26S Proteasome with non-cleavable M1-linked hexaubiquitin and E3 ubiquitin ligase E6AP/UBE3A Deposited 2020-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Tris, pH 7.5, 50 mM NaCl, 1.5 mM ATP-gamma-S, 5 mM MgCl2, 2 mM DTT, 10 uM zinc sulfate
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric
Chain F 1–76（76 aa）
Chain T 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6WTG SdeA DUB Domain in complex with Ubiquitin Deposited 2020-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1 M bicine pH 9.0, 65% (v/v) MPD
Resolution 2.63 Å R-free 0.243
6YPT X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin Deposited 2020-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–151（75 aa）
Not recorded GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；21% PEG-20K + 0.1M MES-NaOH pH6.5
Resolution 3.66 Å R-free 0.283
6YPT X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin Deposited 2020-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–151（75 aa）
Not recorded GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；21% PEG-20K + 0.1M MES-NaOH pH6.5
Resolution 3.66 Å R-free 0.283
6Z7V Crystal structure of Mindy2 (C266A) in complex with Lys48 linked di-ubiquitin (K48-Ub2) Deposited 2020-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Not recorded K POTASSIUM ION × 4 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；50 mM potassium phosphate monobasic, 14% PEG 8000
Resolution 2.65 Å R-free 0.254
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain U 1–75（75 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–75（75 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain U 1–75（75 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Mutation：G75A, G76A ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K
Resolution 2.20 Å R-free 0.252
7BBF Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2 Deposited 2020-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–76（76 aa）
Chain F 1–76（76 aa）
Chain I 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M bicine Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2 % of each Anesthetic alkaloids (lidocaine HCl H2O, procaine HCl, proparacaine HCl, tetracaine HCl)
Resolution 2.54 Å R-free 0.253
7BXG MavC-UBE2N-Ub complex Deposited 2020-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M sodium malonate, pH 7.0, 12% PEG3350
Resolution 2.71 Å R-free 0.243
7EAL The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin Deposited 2021-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；255 K；0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400
Resolution 2.50 Å R-free 0.224
7EAL The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin Deposited 2021-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–152（152 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；255 K；0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400
Resolution 2.50 Å R-free 0.224
7EAO The structure of the A20-binding inhibitor of NF-kB 1 in complex with tri-ubiquitin Deposited 2021-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–228（228 aa） Fragment：UNP residues 1-228
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Potassium citrate tribasic, 20% PEG 3350
Resolution 2.90 Å R-free 0.283
7EB9 The structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin Deposited 2021-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–304（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M Sodium malonate pH 6.0, 10% PEG 3350
Resolution 3.20 Å R-free 0.264
7JXV ANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia protein) bound to ubiquitin Deposited 2020-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES, pH 6, 0.2 M NaCl, 20% w/v MPEG2000
Resolution 2.35 Å R-free 0.264
7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7KEO Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment Deposited 2020-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M phosphate-citriate, 40% v/v Polyethylene glycol 300
Resolution 2.90 Å R-free 0.282
7KEO Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment Deposited 2020-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M phosphate-citriate, 40% v/v Polyethylene glycol 300
Resolution 2.90 Å R-free 0.282
7M4M Crystal structure of RBR E3 ligase RNF216 with ubiquitin Deposited 2021-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 5 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；15% PEG 6000, 0.18 M NaCl, 0.09 M Na HEPES pH7.0, 0.1 M KCl
Resolution 2.39 Å R-free 0.247
7M4M Crystal structure of RBR E3 ligase RNF216 with ubiquitin Deposited 2021-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；15% PEG 6000, 0.18 M NaCl, 0.09 M Na HEPES pH7.0, 0.1 M KCl
Resolution 2.39 Å R-free 0.247
7M4N Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin Deposited 2021-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；0.2M ammonium sulfate, 30% PEG 4000
Resolution 2.52 Å R-free 0.273
7M4N Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin Deposited 2021-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；0.2M ammonium sulfate, 30% PEG 4000
Resolution 2.52 Å R-free 0.273
7M4O Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin Deposited 2021-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 3 SO4 SULFATE ION × 3 GOL GLYCEROL × 3 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.22；293 K；0.259 M ammonium sulfate, 30.1 % PEG monomethyl ether 2000, 0.1M sodium acetate-acetic acid pH 5.22
Resolution 2.21 Å R-free 0.252
7MEX Structure of yeast Ubr1 in complex with Ubc2 and N-degron Deposited 2021-04-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7MIC Maize rayado fino virus protease in complex with Ubiquitin Deposited 2021-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.8；277 K；100 mM phosphate citrate buffer (pH 3.8), 200 mM lithium sulfate and 25 % PEG 1000
Resolution 2.09 Å R-free 0.263
7MYF Ubiquitin variant UbV.k.1 in complex with Ube2k Deposited 2021-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2-0.3 M ammonium citrate dibasic, 20-25% PEG3350
Resolution 3.00 Å R-free 0.293
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain N 1–76（76 aa）
Chain O 1–76（76 aa）
Chain P 1–76（76 aa）
Chain Q 1–76（76 aa）
Chain R 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain T 1–76（76 aa）
Chain U 1–76（76 aa）
Chain V 1–76（76 aa）
Chain W 1–76（76 aa）
Chain X 1–76（76 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Z 1–76（76 aa）
Chain a 1–76（76 aa）
Chain b 1–76（76 aa）
Chain c 1–76（76 aa）
Chain d 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain f 1–76（76 aa）
Chain g 1–76（76 aa）
Chain h 1–76（76 aa）
Chain i 1–76（76 aa）
Chain j 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain l 1–76（76 aa）
Chain m 1–76（76 aa）
Chain n 1–76（76 aa）
Chain o 1–76（76 aa）
Chain p 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt 0.1 M BICINE pH 8.5 15% w/v PEG 20,000
Resolution 2.81 Å R-free 0.288
7OWD Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；291 K；40 (v/v) PEG 300, 100 mM phosphate/citrate pH 4.2
Resolution 1.71 Å R-free 0.245
7R70 Crystal Structure of the UbArk2C fusion protein Deposited 2021-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.15 K；1.6 M tri-sodium citrate
Resolution 2.50 Å R-free 0.245
7R70 Crystal Structure of the UbArk2C fusion protein Deposited 2021-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.15 K；1.6 M tri-sodium citrate
Resolution 2.50 Å R-free 0.245
7R71 Crystal Structure of the UbArk2C-UbcH5b~Ub complex Deposited 2021-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M MMT pH 6.0, 25% w/v PEG 1500
Resolution 2.80 Å R-free 0.271
7TV4 Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 77–228（152 aa）
Chain G 77–228（152 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5, 22% v/v PEG Smear Broad
Resolution 4.20 Å R-free 0.286
7UV5 The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M sodium tartrate, 15% PEG3350
Resolution 1.45 Å R-free 0.179
7UYH Structure of the first OTU domain from Legionella pneumophila effector protein LotA bound to K6-linked diUb Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；25% PEG 3350, 10% ethylene glycol, 0.2 M KSCN, 0.1 M MES pH 5.5
Resolution 2.80 Å R-free 0.262
7YUI Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 77–380（304 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Lithium chloride, 0.1 M Tris(pH 8), 20 %(w/v)PEG 8000
Resolution 2.60 Å R-free 0.258
7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 76–152（77 aa）
Chain L 76–152（77 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5 10% (w/v) PEG 8K
Resolution 2.53 Å R-free 0.258
7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 76–152（77 aa）
Chain I 76–152（77 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5 10% (w/v) PEG 8K
Resolution 2.53 Å R-free 0.258
8A9J Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction) Deposited 2022-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3.0 secs before plunging
Resolution 2.80 Å
8A9K Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction) Deposited 2022-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8AMS Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin Deposited 2022-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 76–152（77 aa）
Not recorded GOL GLYCEROL × 9 ZN ZINC ION × 4 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.2 M sodium formate, 0.1 M bis-tris propane, 20% PEG 3350
Resolution 2.40 Å R-free 0.233
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–76（76 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain U 1–76（76 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8E7O CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN Deposited 2022-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：K48R SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；25% w/v PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5
Resolution 1.70 Å R-free 0.221
8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–76（76 aa）
Chain G 1–76（76 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2
Resolution 3.08 Å R-free 0.266
8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2
Resolution 3.08 Å R-free 0.266
8EB0 RNF216/E2-Ub/Ub transthiolation complex Deposited 2022-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 7 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；2 M ammonium sulfate
Resolution 3.03 Å R-free 0.339
8FTQ Crystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44 Deposited 2023-01-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–72（72 aa）
Chain D 1–72（72 aa）
Not recorded ZTO N-(3-{[(3R)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)-4-methoxybenzamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 4.6；277 K；0.1 M Citric acid pH 4.6 and 20% PEG4000
Resolution 2.10 Å R-free 0.247
8K6I LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded PO4 PHOSPHATE ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Sodium Chloride, PEG8000, HEPES
Resolution 3.19 Å R-free 0.315
8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain Fa 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；blot force = 0 N blot time = 8 s
Resolution 3.40 Å
8PJN Catalytic module of human CTLH E3 ligase bound to multiphosphorylated UBE2H~ubiquitin Deposited 2023-06-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8PMQ Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin Deposited 2023-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain U 1–76（76 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
8PQL K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide Deposited 2023-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: nonameric
Chain E 1–685（685 aa）
Chain U 1–685（685 aa）
Mutation：K48C,S455P L456T L457Q K458G E459R L460A Mutation：K48C SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.76 Å
8Q7R Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide Deposited 2023-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–685（685 aa）
Not recorded U9O 5-azanyl-1-oxidanyl-pentan-2-one × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.71 Å
8R5H Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Deposited 2023-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–75（75 aa）
Not recorded ZN ZINC ION × 3 SY8 5-azanylpentan-2-one × 1 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.44 Å
8SSI Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin Deposited 2023-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 5.6
Resolution 2.50 Å R-free 0.254
8SSI Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin Deposited 2023-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 5.6
Resolution 2.50 Å R-free 0.254
8ST7 Structure of E3 ligase VsHECT bound to ubiquitin Deposited 2023-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20% PEG 2K MME, 0.1 M MES pH 6.0, and 20% ethylene glycol
Resolution 1.44 Å R-free 0.199
8ST7 Structure of E3 ligase VsHECT bound to ubiquitin Deposited 2023-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；20% PEG 2K MME, 0.1 M MES pH 6.0, and 20% ethylene glycol
Resolution 1.44 Å R-free 0.199
8ST8 Structure of E3 ligase SopA bound to ubiquitin Deposited 2023-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；22.5% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 7.0, and 20% glycerol
Resolution 1.75 Å R-free 0.196
8ST9 Structure of E3 ligase NleL bound to ubiquitin Deposited 2023-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 3350, 0.2 M KSCN, 0.1 M bis-tris propane pH 7.5, 20% glycerol, and 10% ethylene glycol
Resolution 2.50 Å R-free 0.252
8ST9 Structure of E3 ligase NleL bound to ubiquitin Deposited 2023-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 3350, 0.2 M KSCN, 0.1 M bis-tris propane pH 7.5, 20% glycerol, and 10% ethylene glycol
Resolution 2.50 Å R-free 0.252
8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain M 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8T48 The N4BP1 CUE-like domain in complex with linear di-Ubiquitin Deposited 2023-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–152（152 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH 8.5, 30% (w/v) PEG 4K, 0.2 M Li2SO4
Resolution 2.00 Å R-free 0.218
8T48 The N4BP1 CUE-like domain in complex with linear di-Ubiquitin Deposited 2023-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa）
Not recorded LI LITHIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH 8.5, 30% (w/v) PEG 4K, 0.2 M Li2SO4
Resolution 2.00 Å R-free 0.218
8U5H Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Deposited 2023-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9D1Y Structure of G75R Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Mutation：G75R GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10%PEG5KMME, 5% Tacsimate pH=7.0, 0.1M HEPES pH=7.0
Resolution 2.60 Å R-free 0.216
9D1Z Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Mutation：G75Q MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10%%KMME, 5% Tacsimate pH=7.0, 0.1M HEPES 7.0
Resolution 1.88 Å R-free 0.190
9D8P Focused map of Cryo-EM structure of Ubiquitin C-degron bound to KLHDC10-EloB/C Deposited 2024-08-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DI1 Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279 Deposited 2024-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9DI2 Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex Deposited 2024-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9DNS Cryo-EM structure of Tom1-UBE2D2-ubiquitin complex Deposited 2024-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain U 1–76（76 aa）
Chain V 1–76（76 aa）
Chain W 1–76（76 aa）
Chain X 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；30 mM HEPES pH 7.2, 200 mM NaCl, 0.5 mM TCEP, 0.2 mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO detergent added to final conc. of 0.2 mM. Sample applied twice.
Resolution 2.80 Å
9EGV HOIL-1 RING2 domain bound to ubiquitin Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 76–152（77 aa）
Not recorded ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.2, 1.8 M lithium sulfate monohydrate
Resolution 2.00 Å R-free 0.208
9EGV HOIL-1 RING2 domain bound to ubiquitin Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: dimeric
Chain C 76–152（77 aa）
Not recorded ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.2, 1.8 M lithium sulfate monohydrate
Resolution 2.00 Å R-free 0.208
9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 76–152（77 aa）
Not recorded ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4
Resolution 1.78 Å R-free 0.182
9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 76–152（77 aa）
Not recorded ZN ZINC ION × 3 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4
Resolution 1.78 Å R-free 0.182
9ERZ Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide Deposited 2024-03-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–150（74 aa）
Chain D 77–150（74 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Bis-Tris Propane, pH 6.0, 0.2 M sodium fluoride, and 20% (v/v) PEG 3350
Resolution 2.02 Å R-free 0.229
9FCI USP1 bound to KSQ-4279 and ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2024-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9FCJ USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (ordered subset, focused refinement) Deposited 2024-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blotting for 3.0 seconds
Resolution 2.70 Å
9FJ3 Structure of ubiquitin bound of coiled-coil UIM form 2 Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 77–152（76 aa）
Not recorded A1IDH 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)
Resolution 1.40 Å R-free 0.238
9FJ3 Structure of ubiquitin bound of coiled-coil UIM form 2 Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 77–152（76 aa）
Not recorded A1IDH 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)
Resolution 1.40 Å R-free 0.238
9FJ4 Structure of ubiquitin bound to coiled coil-UIM form 1 Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 77–152（76 aa）
Mutation：contain GSGGS at the N-terminus A1IDH 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)
Resolution 1.54 Å R-free 0.266
9GKN Structure of HECT E3 TRIP12 forming K29-linked Ubiquitin chains Deposited 2024-08-25 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa）
Chain C 77–152（76 aa）
Mutation：K29C SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
9KHS Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation) Deposited 2024-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K48C Mutation：K29R No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
9KHT cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation) Deposited 2024-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain D 1–76（76 aa）
Chain d 1–76（76 aa）
Mutation：K48C Mutation：K48C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.85 Å
9M7O Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation) Deposited 2025-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K48C Mutation：K29R No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9MC4 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4 Deposited 2025-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9MC5 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 3 Deposited 2025-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å
9N1F Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex Deposited 2025-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium Malonate and 18% w/v PEG 3350
Resolution 2.10 Å R-free 0.279
9O4M Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine Deposited 2025-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded 6NA HEXANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
Resolution 2.00 Å R-free 0.262
9O4M Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine Deposited 2025-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded 6NA HEXANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
Resolution 2.00 Å R-free 0.262
9OVX CRYSTAL STRUCTURE OF UBIQUITIN K27M MUTANT Deposited 2025-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：K27M CD CADMIUM ION × 6 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；CdCl2 (0.2 M), PEG400 (10% v/v), 2-methyl-2,4-pentanediol (12% v/v) and sodium acetate buffer (0.1 M, pH 4.6)
Resolution 1.50 Å R-free 0.154
9QGG Consensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex Deposited 2025-03-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
9QGI Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 2) Deposited 2025-03-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9QGR Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4) Deposited 2025-03-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9QGW Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (singly loaded) Deposited 2025-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9QH5 Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded) Deposited 2025-03-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9QIA Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 2) Deposited 2025-03-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
9R85 Cryo-EM structure of the E3 ligase HECTD3 conjugated to ubiquitin Deposited 2025-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain U 1–75（75 aa）
Not recorded ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.97 Å
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain U 1–75（75 aa）
Not recorded FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9YEA Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant Deposited 2025-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1 M Sodium Citrate, 20 % (w/v) PEG 3000
Resolution 1.83 Å R-free 0.239

219 other PDB entries and 348 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBC_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain B； PDBConstruct 1–75； UniProt 1–75 Author chain C； PDBConstruct 1–76； UniProt 1–76

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 1–76 Mutation：K48R Ubiquitin × 1 （P0CG48） Polyubiquitin-C × 1 （P0CG48） Isoform 3 of E3 ubiquitin-protein ligase TRIP12 × 1 （Q14669） SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.69 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9GKM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP P0CG47 residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2MRO Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1) Deposited 2014-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Human Ubiquitin
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298.2 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2MSG Solid-state NMR structure of ubiquitin Deposited 2014-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–78（72 aa） Fragment：UNP residuse 1-72
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 273 K；Pressure ambient
NMR sample composition 20 mg [U-100% 13C; U-100% 15N] Ubiquitin, 30 mg [1-glucose 13C,U-100% 15N] Ubiquitin, 40 mg [2-glucose 13C,U-100% 15N] Ubiquitin, 40 % v/v MPD, 0.2 M CdCl2, 1 mg DSS, 100% H20 | 100% H20
Resolution not provided
2N13 Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb Deposited 2015-03-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.5 mM [U-13C; U-15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa） Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
Resolution 2.70 Å R-free 0.279
2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–152（152 aa） Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
Resolution 2.70 Å R-free 0.279
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Chain C 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Chain D 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3ONS Crystal structure of Human Ubiquitin in a new crystal form Deposited 2010-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–72（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；277 K；2 ul of a 10 mg/ml protein solution was mixed with 2 ul of the reservoir solution (50-56 % MPD and 8-18 % (v/v) glycerol solution in 27mM sodium citrate (pH 4.0-4.2) buffer), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.211
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：YES Mutation：YES ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Mutation：YES ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：YES ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZNH Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl. Deposited 2013-02-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；20-30% PEG 8000, 100 MM NA CACODYLATE PH 6.5, 100 MM MG ACETATE, AND 2% N-OCTYL-BETA-D-GLUCOSIDE.
Resolution 2.30 Å R-free 0.275
4UEL UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain Deposited 2014-12-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS
Resolution 2.30 Å R-free 0.234
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa） Fragment：unp residues 1-76
Chain F 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
Resolution 8.30 Å R-free 0.337
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–76（76 aa） Fragment：unp residues 1-76
Chain L 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
Resolution 8.30 Å R-free 0.337
4WLR Crystal Structure of mUCH37-hRPN13 CTD-hUb complex Deposited 2014-10-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；277 K；25% PEG 3350, 220 mM MgCl2,100 mM Bis-Tris
Resolution 2.00 Å R-free 0.227
4WUR The crystal structure of the MERS-CoV papain-like protease (C111S) with human ubiquitin Deposited 2014-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded IPA ISOPROPYL ALCOHOL × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；291 K；22% w/v PEG 4000, 15% v/v 2-propanol, 0.1M tri-sodium citrate pH 4.8 and 10% glycerol
Resolution 3.16 Å R-free 0.252
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4XOF Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin crystals without Zinc. Deposited 2015-01-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0
Resolution 1.15 Å R-free 0.171
4ZFR Catalytic domain of Sst2 F403A mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol
Resolution 1.72 Å R-free 0.237
4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
Resolution 2.30 Å R-free 0.235
4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
Resolution 2.30 Å R-free 0.235
4ZPZ Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys Deposited 2015-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–73（73 aa） Fragment：ubiquitin, UNP residues 1-73
Chain B 1–73（73 aa） Fragment：ubiquitin, UNP residues 1-73
Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；50 mM sodium cacodylate, 25% PEG 4000
Resolution 1.54 Å R-free 0.173
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain X 1–76（76 aa）
Chain c 1–76（76 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain h 1–76（76 aa）
Chain m 1–76（76 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Resolution 2.62 Å R-free 0.260
5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Resolution 2.62 Å R-free 0.260
5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded SO4 SULFATE ION × 6 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
Resolution 2.64 Å R-free 0.236
5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded SO4 SULFATE ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
Resolution 2.64 Å R-free 0.236
5CVM USP46~ubiquitin BEA covalent complex Deposited 2015-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–59（59 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；3.6 M sodium formate
Resolution 1.90 Å R-free 0.197
5CVN WDR48 (2-580):USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；292 K；0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8
Resolution 3.36 Å R-free 0.222
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
Resolution 3.88 Å R-free 0.275
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
Resolution 3.88 Å R-free 0.275
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0M Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；SPG buffer, PEG 1500
Resolution 1.91 Å R-free 0.213
5DFL Crystal structure of Ube2K~Ubiquitin conjugate Deposited 2015-08-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M di-ammonium citrate pH 5.0, 20% PEG 3350
Resolution 2.10 Å R-free 0.235
5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–75（74 aa） Fragment：Ubiquitin, UNP residues 2-75
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.32 Å R-free 0.201
5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–75（74 aa） Fragment：Ubiquitin, UNP residues 2-75
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.32 Å R-free 0.201
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ACT ACETATE ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EYA TRIM25 RING domain in complex with Ubc13-Ub conjugate Deposited 2015-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li citrate, 20% PEG 3350
Resolution 2.40 Å R-free 0.228
5GJQ Structure of the human 26S proteasome bound to USP14-UbAl Deposited 2016-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging
Resolution 4.35 Å
5GO7 Linear tri-ubiquitin Deposited 2016-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M sodium dihydrogen phosphate, 20% PEG 3350, PH 6.0
Resolution 1.80 Å R-free 0.310
5GO8 Linear tetra-ubiquitin Deposited 2016-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Sodium acetate trihydrate, 20% PEG 3350, PH8.0
Resolution 2.21 Å R-free 0.322
5GOB Lys6-linked di-ubiquitin Deposited 2016-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；289 K；0.2M Magnesium chloride hexahydrate, 20% PEG 3350, PH5.9
Resolution 1.15 Å R-free 0.229
5GOC Lys11-linked diubiquitin Deposited 2016-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Li2SO4, 0.1M tris 8.5, 30% PEG 4000
Resolution 1.73 Å R-free 0.235
5GOD Lys27-linked di-ubiquitin Deposited 2016-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate PH6.5, 20% PEG 8000
Resolution 1.15 Å R-free 0.222
5GOG Lys29-linked di-ubiquitin Deposited 2016-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Potassium sulfate, 20% PEG 3350
Resolution 1.98 Å R-free 0.330
5GOH Lys33-linked di-ubiquitin Deposited 2016-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium sulfate heptahydrate, 20% peg 3350
Resolution 1.95 Å R-free 0.271
5GOI Lys48-linked di-ubiquitin Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Sodium citrate tribasic dehydrate PH5.6, 20% 2-Propanol, 20%PEG 4000
Resolution 1.59 Å R-free 0.311
5GOJ Lys63-linked di-ubiquitin Deposited 2016-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M TRIS hydrochloride PH8.5, 2.0M Ammonium phosphate monobasic
Resolution 1.55 Å R-free 0.253
5GOK K11/K63-branched tri-Ubiquitin Deposited 2016-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M MgSO4, 20% PEG 3350, 4mM CdCl2, PH6.0
Resolution 1.84 Å R-free 0.245
5H7S Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain Deposited 2016-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350
Resolution 3.49 Å R-free 0.286
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 75–150（76 aa） Fragment：UNP residues 75-150
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 75–150（76 aa） Fragment：UNP residues 75-150
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IFR Structure of the stable UBE2D3-UbDha conjugate Deposited 2016-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200mM tripotassium citrate, 20% PEG 3350
Resolution 2.20 Å R-free 0.243
5J8P Lys27-linked diubiquitin Deposited 2016-04-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate, pH 6.5, 20% PEG 8000
Resolution 1.55 Å R-free 0.295
5JBV Lys27-linked triubiquitin Deposited 2016-04-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
Resolution 2.10 Å R-free 0.306
5JBY Lys27-linked triubiquitin Deposited 2016-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
Resolution 1.99 Å R-free 0.308
5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 76–154（79 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
Resolution 2.00 Å R-free 0.220
5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 76–154（79 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
Resolution 2.00 Å R-free 0.220
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
Resolution 3.32 Å R-free 0.209
5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–76（76 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
Resolution 3.32 Å R-free 0.209
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5K9P Ser20 phosphorylated ubiquitin Deposited 2016-06-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；45% (w/v) PEG 400, 100 mM tris-HCl
Resolution 1.55 Å R-free 0.219
5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
Resolution 4.54 Å
5KHY Crystal structure of oxime-linked K6 diubiquitin Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–73（73 aa）
Chain B 1–75（75 aa）
Mutation：Unnatural aminoxylysine amino acid at position 6 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：unnatural residue 76 oxime linked to chain A ZN ZINC ION × 10 ETA ETHANOLAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, Zinc acetate
Resolution 3.50 Å R-free 0.331
5KYC Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound) Deposited 2016-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded MLA MALONIC ACID × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；8% tacsimate pH 4.0, 20% PEG3350
Resolution 1.43 Å R-free 0.192
5KYD Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.2M Ammonium fluoride, 20% PEG3350
Resolution 1.62 Å R-free 0.213
5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
Resolution 1.97 Å R-free 0.223
5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
Resolution 1.97 Å R-free 0.223
5KYF Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350
Resolution 1.45 Å R-free 0.185
5L8H Structure of USP46-UbVME Deposited 2016-06-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.96M Sodium Citrate pH7.5 and 0.1mM zinc chloride Cryo - 20% Glycerol
Resolution 1.85 Å R-free 0.194
5L8W Structure of USP12-UB-PRG/UAF1 Deposited 2016-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP. Cryo- 30% Glycerol
Resolution 2.79 Å R-free 0.259
5L9T Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density Deposited 2016-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 22 PDB declaration: 22-meric
Chain S 77–153（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
5LN1 STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; Deposited 2016-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain U 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION, RECRYSTALLIZATION；pH 6.5；292 K；12% (W/V) PEG 20000, 0.1M MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
Resolution 3.14 Å R-free 0.248
5LRV Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–75（75 aa）
Mutation：K11X Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride
Resolution 2.80 Å R-free 0.244
5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
Resolution 2.00 Å R-free 0.217
5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
Resolution 2.00 Å R-free 0.217
5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
Resolution 2.85 Å R-free 0.246
5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
Resolution 2.85 Å R-free 0.246
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 76–152（77 aa）
Mutation：M1S SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 76–152（77 aa）
Mutation：M1S SO4 SULFATE ION × 1 RIB alpha-D-ribofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 76–152（77 aa）
Mutation：M1S RIB alpha-D-ribofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 77–152（76 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5N2W WT-Parkin and pUB complex Deposited 2017-02-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 CL CHLORIDE ION × 1 TMO trimethylamine oxide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
Resolution 2.68 Å R-free 0.243
5N38 S65DParkin and pUB complex Deposited 2017-02-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
Resolution 2.60 Å R-free 0.236
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 3 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 4 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 ETF TRIFLUOROETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NVG Thr12 Phosphorylated Ubiquitin Deposited 2017-05-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；291.15 K；20% (v/v) ethanol, 20% (w/v) PEG-1000, 0.1M Phosphate-citrate pH 4.2
Resolution 1.07 Å R-free 0.167
5O44 Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages. Deposited 2017-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–74（74 aa）
Chain C 1–74（74 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Mutation：Deleted for Gly 75 and Gly 76 Mutation：Deleted for Gly 75 and Gly 76 Mutation：K48R Mutation：K48R SO4 SULFATE ION × 18 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3M MgSo4 and 100mM MES monohydrate pH 6.5
Resolution 3.14 Å R-free 0.254
5O6T BIRC4 RING in complex with dimeric ubiquitin variant Deposited 2017-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 75–150（76 aa）
Chain D 75–150（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；0.1 M NaHEPES pH 7.5, 1.4 M tri-Na citrate
Resolution 1.57 Å R-free 0.183
5OHK Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) Deposited 2017-07-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate
Resolution 2.34 Å R-free 0.261
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 1–76（76 aa）
Chain P 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
Resolution 3.60 Å R-free 0.253
5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
Resolution 3.60 Å R-free 0.253
5OHP Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.73 M sodium citrate, 0.1 M Hepes pH 7.0
Resolution 2.80 Å R-free 0.249
5TOF Room temperature structure of ubiquitin variant u7ub25 Deposited 2016-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1ul protein solution at 20 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.6, 2.6 M ammonium sulfate)
Resolution 1.12 Å R-free 0.175
5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
Resolution 1.08 Å R-free 0.121
5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
Resolution 1.08 Å R-free 0.121
5TUT UbcH5a-Ub isopeptide conjugate Deposited 2016-11-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；Hampton PEG/Ion F10
Resolution 2.60 Å R-free 0.243
5UJL Representative 1-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Chain B 1–76（76 aa） Fragment：residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5UJN Representative 2-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 150 uM [U-99% 15N] distal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 150 uM [U-99% 15N] proximal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULH Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM potassium thiocyanate, 20% PEG 3350
Resolution 1.95 Å R-free 0.217
5ULK Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM ammonium nitrate, 20% PEG 3350
Resolution 2.38 Å R-free 0.267
5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.42 Å R-free 0.175
5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.42 Å R-free 0.175
5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
Resolution 2.00 Å R-free 0.182
5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
Resolution 2.00 Å R-free 0.182
5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
Resolution not provided
5VF0 Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin Deposited 2017-04-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] RAD18, 3 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM RAD18, 0.6 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM [U-100% 15N] RAD18, 1.0 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM RAD18, 0.2 mM [U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
Resolution 3.41 Å R-free 0.294
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
Resolution 3.41 Å R-free 0.294
5VO0 Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5
Resolution 3.90 Å R-free 0.299
5VZM Solution NMR structure of human Rev1 (932-1039) in complex with ubiquitin Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 1
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 20 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Rev1, 3 mM Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM Rev1, 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VZW TRIM23 RING domain in complex with UbcH5-Ub Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bis-Tris, pH 5.5, 0.2 M calcium chloride, 17% w/v PEG3350
Resolution 2.28 Å R-free 0.237
5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：S65D MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
Resolution 1.18 Å R-free 0.190
5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：S65D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
Resolution 1.18 Å R-free 0.190
5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Resolution 1.85 Å R-free 0.197
5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Resolution 1.85 Å R-free 0.197
5X3M crystal structure of p-Ub-S65-NH2 Deposited 2017-02-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Lithium Sulfate monohydrate, 0.1M HEPES pH 7.5, 25%(w/v) Polyethylene Glycol 3350
Resolution 1.82 Å R-free 0.271
5X3N Crystal structure of DiUb-K6 Deposited 2017-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium formate dihydrate, 20%(w/v) Polyethylene glycol 3350
Resolution 1.65 Å R-free 0.276
5X3O Crystal structure of p-DiUb-S65-COOH Deposited 2017-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Ammonium phosphate monobasic, 20%(w/v) Polyethylene glycol 3350
Resolution 2.19 Å R-free 0.315
5XBO Lanthanoid tagging via an unnatural amino acid for protein structure characterization Deposited 2017-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded TB TERBIUM(III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 760
NMR sample composition 20mM HEPES, 100mM sodium chloride, 10% D2O, 0.2mM [U-99% 15N] ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20mM HEPES, 100mM sodium chloride, 0.1mM [U-99% 15N] HHR23A UBA1 Domain, 0.1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XDP K11/48-branched teraubiquitin Deposited 2017-03-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；289 K；0.2M Potassium nitrate, 20% w/v Polyethylene glycol 3350
Resolution 2.38 Å R-free 0.271
5XK4 Retracted state of S65-phosphorylated ubiquitin Deposited 2017-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XK5 Relaxed state of S65-phosphorylated ubiquitin Deposited 2017-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.8 mM [U-98% 13C; U-98% 15N] relaxed pUb, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XPK Crystal structure of ubiquitin-k6mimic Deposited 2017-06-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium formate, 20% w/v PEG 3350
Resolution 2.27 Å R-free 0.310
5YIJ Structure of a Legionella effector with substrates Deposited 2017-10-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain G 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
Resolution 3.18 Å R-free 0.275
5YIK Structure of a Legionella effector with its substrate Deposited 2017-10-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain F 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
Resolution 3.10 Å R-free 0.279
5YMY The structure of the complex between Rpn13 and K48-diUb Deposited 2017-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.58 mM [U-13C; U-15N; U-2H] Rpn13, 20 mM MES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 77–152（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 77–152（76 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 77–152（76 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
Resolution 3.20 Å R-free 0.262
5ZD0 Solution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy Deposited 2018-02-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：L8A,I44A,V70A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR measurement conditions pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 50 uM [U-100% 13C; U-100% 15N] human ubiquitin with three alanine mutations 1, 50 uM [U-100% 15N] human ubiquitin with three alanine mutations 2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：K48R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：K48R GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：M77D GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
Resolution 2.36 Å R-free 0.229
6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：residues 1-76
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
Resolution 2.36 Å R-free 0.229
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6CP2 SidC in complex with UbcH7~Ub Deposited 2018-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 75–152（78 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；16% PEG 3000, 0.1 M Tris pH 9.0
Resolution 2.90 Å R-free 0.288
6DGF Ubiquitin Variant bound to USP2 Deposited 2018-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 153–226（74 aa）
Mutation：Q2C, K6C, K11R, T12C ZN ZINC ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES buffer pH 6, 12% (w/v) PEG3350, 0.2M sodium sulfate
Resolution 2.34 Å R-free 0.224
6EI1 Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA Deposited 2017-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；0.2 M sodium malonate pH 5, 20 % PEG 3350
Resolution 1.73 Å R-free 0.203
6FDK Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin Deposited 2017-12-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded CL CHLORIDE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20000
Resolution 1.60 Å R-free 0.203
6FGE Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin Deposited 2018-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 FMT FORMIC ACID × 7 PEG DI(HYDROXYETHYL)ETHER × 1 NH4 AMMONIUM ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；4% v/v Tacsimate pH 5.0 and 12% w/v Polyethylene glycol 3,350.
Resolution 1.74 Å R-free 0.209
6FTX Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain N 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76C GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FYH Disulfide between ubiquitin G76C and the E3 HECT ligase Huwe1 Deposited 2018-03-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C SO4 SULFATE ION × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Zn SO4 0.1M Na Acetat pH 4.0
Resolution 2.91 Å R-free 0.266
6GLC Structure of phospho-Parkin bound to phospho-ubiquitin Deposited 2018-05-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 GOL GLYCEROL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)
Resolution 1.80 Å R-free 0.205
6GZS Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin Deposited 2018-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES (pH 6.0), 20% PEG 6000
Resolution 1.90 Å R-free 0.213
6H4H Usp28 catalytic domain variant E593D in complex with UbPA Deposited 2018-07-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Not recorded SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M Citrate pH 5.0 0.8 M Ammonium Sulfate
Resolution 3.50 Å R-free 0.280
6HEI Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA Deposited 2018-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–151（75 aa）
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；22% (w/v) PEG 3350, 300 mM potassium sodium tartrate
Resolution 1.64 Å R-free 0.214
6HEK Structure of human USP28 bound to Ubiquitin-PA Deposited 2018-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa）
Chain D 77–152（76 aa）
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；8% (w/v) PEG 3350, 200 mM ammonium acetate and 100 mM sodium citrate pH 5.4
Resolution 3.03 Å R-free 0.237
6HPR Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub Deposited 2018-09-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 75–152（78 aa）
Chain D 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium fluoride and 15% (w/v) PEG 3350
Resolution 1.70 Å R-free 0.197
6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl, polyethylene glycol 3350, ammonium acetate.
Resolution 2.47 Å R-free 0.236
6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl, polyethylene glycol 3350, ammonium acetate.
Resolution 2.47 Å R-free 0.236
6ISU Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3 Deposited 2018-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；18% PEG 3350 (w/v), 400 mM Ca(AC)2
Resolution 1.87 Å R-free 0.264
6JB6 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution Deposited 2019-01-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
Resolution 2.70 Å R-free 0.284
6JB7 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A resolution Deposited 2019-01-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
Resolution 2.10 Å R-free 0.250
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain Y 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6K9P Structure of Deubiquitinase Deposited 2019-06-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.05 Å R-free 0.210
6LP2 Structure of Lpg2148/UBE2N-Ub complex Deposited 2020-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, potassium citrate
Resolution 2.48 Å R-free 0.233
6MSB Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6MSD Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6MSE Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6MSG Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 8 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Mutation：G76C Mutation：G76C SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 2.96 Å
6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Chain F 1–77（77 aa）
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
Resolution 2.20 Å R-free 0.230
6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–77（77 aa）
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
Resolution 2.20 Å R-free 0.230
6OQ2 NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–77（77 aa）
Mutation：K11R, K48R, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6PGV Human Josephin-2 in complex with ubiquitin Deposited 2019-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 4.6；293 K；0.1 M sodium acetate pH 4.6, 0.2 M CaCl2, 22.5% (w/v) PEG 6000; microbatch under Al's Oil
Resolution 2.30 Å R-free 0.224
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 77–150（74 aa）
Chain B 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 77–150（74 aa）
Chain D 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 77–150（74 aa）
Chain F 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 77–150（74 aa）
Chain H 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 77–150（74 aa）
Chain J 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain K 77–150（74 aa）
Chain L 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 2 BR BROMIDE ION × 3 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 3 BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6UD0 Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin Deposited 2019-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–77（77 aa）
Mutation：K63R Mutation：+D77 No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1
NMR sample composition 200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
6UYI hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–77（77 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM proximal ubiquitin, 0.72 mM [U-13C] distal ubiquitin, 100% D2O | 100% D2O
Resolution not provided
6UYJ hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–77（77 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
Resolution not provided
6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded PO4 PHOSPHATE ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
Resolution 2.30 Å R-free 0.255
6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded PO4 PHOSPHATE ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
Resolution 2.30 Å R-free 0.255
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain III 75–152（78 aa）
Not recorded ZN ZINC ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain LLL 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
Resolution 3.20 Å R-free 0.234
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
Resolution 3.20 Å R-free 0.234
7CAP Cyclic Lys48-linked triubiquitin Deposited 2020-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；20% PEG 3350, 200 mM zinc acetate
Resolution 1.33 Å R-free 0.174
7DNI MDA5 CARDs-MAVS CARD polyUb complex Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 3.20 Å
7DNJ K63-polyUb MDA5CARDs complex Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.30 Å
7F7X Protein complex between phosphorylated ubiquitin and Ubqln2 UBA Deposited 2021-06-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 20 mM HEPES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded CA CALCIUM ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded CA CALCIUM ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MEY Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron Deposited 2021-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–75（75 aa） Fragment：K48C
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 7 Z3V 2-(ethylamino)ethane-1-thiol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
7MYF Ubiquitin variant UbV.k.1 in complex with Ube2k Deposited 2021-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：Q31F, G21R, T23Y, A57S, K59Q, K74E, E75F, T77F, V81I, L82S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2-0.3 M ammonium citrate dibasic, 20-25% PEG3350
Resolution 3.00 Å R-free 0.293
7MYH Ubiquitin variant UbV.k.2 in complex with Ube2k Deposited 2021-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：K6S, L8F, T9V, K11L, T14M, K63N, E64D, T66I, H68R, L71I, G76L GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M sodium citrate tribasic trihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG3350
Resolution 2.39 Å R-free 0.249
7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
Resolution 2.05 Å R-free 0.219
7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
Resolution 2.05 Å R-free 0.219
7OJX E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis Deposited 2021-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K48C ZN ZINC ION × 2 ME7 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；Crystals were grown in: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.5 and 20 % (w/v) PEG 3350. The crystallization drops were set as a 1:1 mixture of the protein complex solution and the precipitant solution.
Resolution 2.40 Å R-free 0.236
7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7RBR The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2021-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–77（77 aa）
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.2 M di-sodium tartrate, 20% PEG-3350,
Resolution 1.88 Å R-free 0.228
7RMA Structure of the fourth UIM (Ubiquitin Interacting Motif) of ANKRD13D in complex with a high affinity UbV (Ubiquitin Variant) Deposited 2021-07-27 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–79（79 aa）
Not recorded SO4 SULFATE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1M Li2SO4, 0.1M sodium acetate pH 4.5 and 50% PEG 400. Crystals were cryoprotected in this buffer plus 20% ethylene glycol
Resolution 2.00 Å R-free 0.246
7S6O The crystal structure of Lys48-linked di-ubiquitin Deposited 2021-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48R Mutation：Aspartic acid residue added to C terminus (D77) ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；289 K；50 mM acetate, 8.6% PEG2000 MME, 17.1% PEG400
Resolution 1.25 Å R-free 0.175
7UV5 The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2022-04-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Mutation：K48R ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M sodium tartrate, 15% PEG3350
Resolution 1.45 Å R-free 0.179
7W38 Structure of USP14-bound human 26S proteasome in state EA2.0_UBL Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7W39 Structure of USP14-bound human 26S proteasome in state EA2.1_UBL Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3A Structure of USP14-bound human 26S proteasome in substrate-engaged state ED4_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W3B Structure of USP14-bound human 26S proteasome in substrate-engaged state ED5_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7W3C Structure of USP14-bound human 26S proteasome in substrate-engaged state ED0_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7W3F Structure of USP14-bound human 26S proteasome in substrate-engaged state ED1_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7W3G Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3H Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3I Structure of USP14-bound human 26S proteasome in substrate-inhibited state SB_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W3J Structure of USP14-bound human 26S proteasome in substrate-inhibited state SC_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7W3K Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD4_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7W3M Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD5_USP14 Deposited 2021-11-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
Resolution 1.90 Å R-free 0.209
8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
Resolution 1.90 Å R-free 0.209
8C07 Structure of HECT E3 UBR5 forming K48 linked Ubiquitin chains Deposited 2022-12-16 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–75（75 aa）
Chain C 1–76（76 aa）
Chain E 1–75（75 aa）
Chain F 1–76（76 aa）
Mutation：K63R Mutation：K63R ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
Resolution 2.50 Å R-free 0.243
8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–75（75 aa）
Chain I 1–76（76 aa）
Chain K 1–75（75 aa）
Chain L 1–76（76 aa）
Mutation：K63R Mutation：K63R ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
Resolution 2.50 Å R-free 0.243
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded FLC CITRATE ANION × 4 EDO 1,2-ETHANEDIOL × 2 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 GVE METHYL 4-AMINOBUTANOATE × 1 FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8EFW Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；2.8M sodium acetate: HCl pH7
Resolution 2.81 Å
8EFX Structure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.16M Magnesium chloride, 0.08M Tris at pH 8.5, 24% PEG 8000 and 20% glycerol
Resolution 1.85 Å R-free 0.229
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 3 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：D77 added to the C-terminus Mutation：K48R GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
Resolution 1.85 Å R-free 0.298
8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain a 1–76（76 aa）
Chain b 1–76（76 aa）
Chain c 1–76（76 aa）
Mutation：D77 added to the C-terminus Mutation：K48R EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
Resolution 1.85 Å R-free 0.298
8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain O 1–76（76 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Resolution 1.25 Å R-free 0.219
8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Resolution 1.25 Å R-free 0.219
8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
Resolution 3.00 Å R-free 0.284
8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
Resolution 3.00 Å R-free 0.284
8J1P Cryo-EM structure of Ufd4 in complex with K29/48 triUb Deposited 2023-04-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K29C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8JRT Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub. Deposited 2023-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.60 Å
8JTI Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Chain x 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.80 Å
8K0G Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Chain x 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.80 Å
8K6F LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG8000, Sodium Choride, Sodium HEPES
Resolution 3.41 Å R-free 0.243
8K6R LnaB-Actin-PRUb ternary complex in the presence of AMPPNP Deposited 2023-07-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Sodium Chloride, Sodium HEPES, PEG8000
Resolution 2.76 Å R-free 0.261
8K6V LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Magnesium acetate, MOPS, PEG8000
Resolution 2.60 Å R-free 0.307
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
Resolution 2.44 Å R-free 0.235
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
Resolution 2.44 Å R-free 0.235
8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Resolution 1.62 Å R-free 0.198
8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Resolution 1.62 Å R-free 0.198
8RQI Structure of Rhizobium NopD with ubiquitin Deposited 2024-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M imidazole 8.0 and 10% PEG8000
Resolution 1.94 Å R-free 0.199
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain U 1–76（76 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8W31 Crystal structure of parkin (R0RB):2pUb with activator compound Deposited 2024-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa） Fragment：residues 1-75
Chain C 1–75（75 aa） Fragment：residues 1-75
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 A1AE9 (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
Resolution 2.50 Å R-free 0.294
8XEP Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin Deposited 2023-12-12 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM sodium acetate, pH 6.0, 160 mM ammonium sulfate, 21% PEG 4000, 20% glycerol
Resolution 2.95 Å R-free 0.228
9AVT Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded SO4 SULFATE ION × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulphate
Resolution 1.50 Å R-free 0.203
9AVW Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–152（152 aa）
Chain B 1–152（152 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；2.2 M ammonium sulphate, 20% glycerol
Resolution 1.75 Å R-free 0.222
9AZJ Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 1–76（76 aa）
Chain S 1–76（76 aa）
Chain Z 1–76（76 aa）
Mutation：G76C Mutation：G76C Mutation：G76C ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.6；293 K；150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol
Resolution 3.32 Å R-free 0.285
9B0Z Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–152（152 aa）
Chain D 1–152（152 aa）
Chain G 1–152（152 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol
Resolution 2.41 Å R-free 0.270
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–152（152 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–152（152 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9C5E Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 300 uM [U-13C; U-15N] Rcat domain from Parkin, 300 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 800 uM [U-13C; U-15N] Rcat domain from Parkin, 800 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Ubiquitin G75-C3, 300 uM Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9D1I Structure of Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-07 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10%PEG5KMME, 0.1M HEPES pH=7.0, 5% Tascsimate pH=7.0
Resolution 2.00 Å R-free 0.189
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9EBS Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348 Deposited 2024-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ZN ZINC ION × 1 A1BHF 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
Resolution 2.56 Å R-free 0.253
9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
Resolution 2.56 Å R-free 0.253
9F6G Human USP30 chimera bound to Ubiquitin-PA Deposited 2024-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.56 M sodium citrate pH 7.0
Resolution 1.50 Å R-free 0.211
9FN4 DUBS Parachlamydia sp. PcJOS Deposited 2024-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Molecular Dimensions Morpheus B7, 298 K.
Resolution 2.15 Å R-free 0.201
9FPA DUBS Parachlamydia sp. PcJOS orthorhombic crystal form Deposited 2024-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Midas G6. 35 % v/v glycerol ethoxylate, 0.2 M lithium citrate
Resolution 2.18 Å R-free 0.212
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9HNW USP1-UAF1 bound to Lys63-linked diubiquitin Deposited 2024-12-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K63(DAB) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 153–228（76 aa）
Chain D 153–228（76 aa）
Mutation：G76C Mutation：G76C SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 153–228（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 153–228（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9MC6 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 2 Deposited 2025-03-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9MC7 Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 4 Deposited 2025-03-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9MC9 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1 Deposited 2025-03-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9MCB Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 Deposited 2025-03-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
9QHI Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0) Deposited 2025-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
9QUG Structure of a UBC-Ubiquitin conjugate Deposited 2025-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 4 P4K polyethylene glycol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2,000
Resolution 1.80 Å R-free 0.192
9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain M 77–151（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.90 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain O 153–228（76 aa）
Chain P 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.70 Å
9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain O 1–76（76 aa）
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain O 1–76（76 aa）
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

278 other PDB entries and 429 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBB_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–76； UniProt 1–76

Isoform 3 of E3 ubiquitin-protein ligase TRIP12

Homo sapiens

UniProt Q14669

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 478–2040 Not recorded Ubiquitin × 1 （P0CG48） Polyubiquitin-C × 1 （P0CG48） Polyubiquitin-B × 1 （P0CG47） SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.69 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9GKM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9GKN Structure of HECT E3 TRIP12 forming K29-linked Ubiquitin chains Deposited 2024-08-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 478–2040（1563 aa）
Not recorded SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
9KEN cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb Deposited 2024-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 394–1992（1599 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRIPC_HUMAN
Isoform Q14669-3
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 3–1565； UniProt 478–2040

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9gkm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9gkm
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9gkm
Deposition date deposition_date2024-08-25
Structure title titleStructure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains
Keywords keywordsLIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.72 Å
Radius of gyration Rg (electron density) rg_electron40.06 Å
Forward intensity I(0) i0364948000.00
Molecular weight molecular_weight159680.0 kDa
Excluded volume excluded_volume201800 ų
Envelope volume envelope_volume293940 ų
Hydration-shell volume shell_volume61067 ų
Envelope diameter envelope_diameter143.0 Å
Shell Rg shell_rg45.89 Å
Envelope Rg envelope_rg39.23 Å
Shape Rg shape_rg40.06 Å
Total Rg total_rg40.42 Å
Total atoms total_atoms11231
Residues n_residues1446
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.4 Å
Rg (real space) rg_real40.62 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real3.6490e+08
I(0) uncertainty (real space) i0_real_error6.7010e+06
Rg (reciprocal space) rg_reciprocal40.72 Å
I(0) (reciprocal space) i0_reciprocal365000000.0000
Solution quality estimate total_estimate0.6661
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.5 Å
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.357
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50110000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 1.000; Smooth: 0.867
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)