3wxe

Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin

Method: X-RAY DIFFRACTION D_max: 72.0 Å Quality: EXCELLENT

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

Uncharacterized protein

Danio rerio

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 578–780 Chain A； UniProt 850–951	Fragment：USP domain, UNP residues 578-780, Linker, 850-951 Mutation：C596S, B-box deletion	Ubiquitin × 1 （P0CG48）	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

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 3WXE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WXF Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin Deposited 2014-07-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 578–780（203 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951 Chain A 850–951（102 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951	Mutation：C596S, E674Q, B-box deletion Mutation：C596S, E674Q, B-box deletion	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 578–780（203 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951 Chain C 850–951（102 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951	Mutation：C596S, E674Q, B-box deletion Mutation：C596S, E674Q, B-box deletion	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
3WXG Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin Deposited 2014-07-30	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 578–780（203 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951 Chain A 850–951（102 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951	Mutation：C596A, B-box deletion Mutation：C596A, B-box deletion	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M sodium malonate buffer, 18% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.246
3WXG Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin Deposited 2014-07-30	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 578–780（203 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951 Chain D 850–951（102 aa） Fragment：USP domain, UNP residues 578-780, Linker, 850-951	Mutation：C596A, B-box deletion Mutation：C596A, B-box deletion	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M sodium malonate buffer, 18% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.246

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	E7FEV5_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–206； UniProt 578–780 Author chain A； PDBConstruct 211–312； UniProt 850–951

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–148	Not recorded	Uncharacterized protein × 1 （E7FEV5）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3WXE	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 method 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 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
3WXF Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin Deposited 2014-07-30	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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 experimental method 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 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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）	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 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 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 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 oligomeric state Different ligand/ion 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 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 oligomeric state 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 oligomeric state 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 method 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 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 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 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	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 oligomeric state Different ligand/ion 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 oligomeric state 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 ligand/ion 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 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	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 oligomeric state Different ligand/ion 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–73（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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 oligomeric state 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 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 oligomeric state 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 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 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 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 oligomeric state 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 experimental method 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 oligomeric state Different experimental method 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 method 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 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	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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 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 ligand/ion 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 ligand/ion 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 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 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 method 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 method 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 oligomeric state 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）	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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 oligomeric state 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）	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 ligand/ion 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 oligomeric state 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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）	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 oligomeric state Different ligand/ion 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 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 oligomeric state Different experimental method 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 oligomeric state 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 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 oligomeric state 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 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 experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method 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 × 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 experimental method 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 ligand/ion 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 ligand/ion 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 oligomeric state Different experimental method 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 oligomeric state 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：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 oligomeric state 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：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 oligomeric state 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：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 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 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 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 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 experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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
9GKM Structure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains Deposited 2024-08-25	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 × 4 PDB declaration: tetrameric	Chain B 1–75（75 aa） Chain C 1–76（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 3.69 Å
9GKN Structure of HECT E3 TRIP12 forming K29-linked Ubiquitin chains Deposited 2024-08-25	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 × 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 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） 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 experimental method 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 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） 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 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	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 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	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 oligomeric state 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）	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 ligand/ion 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 ligand/ion 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 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	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 oligomeric state 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 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 oligomeric state 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 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 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	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 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 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 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 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 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–148； UniProt 1–148

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3wxe
Deposition date deposition_date	2014-07-30
Structure title title	Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
Keywords keywords	ubiquitin protease, HYDROLASE-PROTEIN BINDING complex; HYDROLASE/PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.45 Å
Radius of gyration Rg (electron density) rg_electron	22.21 Å
Forward intensity I(0) i0	42552000.00
Molecular weight molecular_weight	51512.0 kDa
Excluded volume excluded_volume	65024 Å³
Envelope volume envelope_volume	76444 Å³
Hydration-shell volume shell_volume	27930 Å³
Envelope diameter envelope_diameter	74.4 Å
Shell Rg shell_rg	30.04 Å
Envelope Rg envelope_rg	22.52 Å
Shape Rg shape_rg	22.20 Å
Total Rg total_rg	23.20 Å
Total atoms total_atoms	3617
Residues n_residues	449
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	72.0 Å
Rg (real space) rg_real	23.30 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	4.2550e+07
I(0) uncertainty (real space) i0_real_error	4.5640e+05
Rg (reciprocal space) rg_reciprocal	23.34 Å
I(0) (reciprocal space) i0_reciprocal	42550000.0000
Solution quality estimate total_estimate	0.9029
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.431
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11000000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	35991.5 kDa
Mutation mutation	C596S, B-box deletion
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3664

SHMGLEVMVGKKKGIQGHYNSSYLDSTLFCLFSFSSVLDTVLLRPRSKTDVEYYKETQELLRTEIVNPLRIHGYVCATKIMKLRRILEKVEAASGFTSEEKDPEEFLNILFHHILRVDPLLRLRSAGQKVQDCYFYQIFMDKKDKVMVPTSQQLLEWSFINSDLKFAEAPSCLIIQMPRFGKDFKMFNKIFPSLELDITDLLDDTPLEGGPHQQMELFAVLCIETSHYVAFVKYGSADSAWLFFDSMADRDGGQNGFNIPQVSRCPEVGEYLKMTPEELHALDPKNIQGYARRLLCDAYMCMYQSPTMSLYK

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	zebra fish
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	16751.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wxeb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d3wxeb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (1 domains)

Domain ID domain_id	3wxeA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	64.676 Å
Unit-cell length b length_b	49.788 Å
Unit-cell length c length_c	71.003 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1852
R_work r_work	0.1819
R_free r_free	0.2472

fit	/app/data/saxs_computation/wx/3wxe/3wxe.fit
pddf	/app/data/pr_computation/wx/3wxe/3wxe.pr.out
profile	/app/data/saxs_computation/wx/3wxe/3wxe.dat

Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin

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

Uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)