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8z36

Crystal structure of HOIP PUB domain in complex with sertraline complex

Method: X-RAY DIFFRACTION Dmax: 84.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase RNF31

Homo sapiens

UniProt Q96EP0

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 4–179 Chain B； UniProt 4–179 Chain C； UniProt 4–179 Not recorded SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；20 mM Na3PO4, 20 mM K3PO4, pH 7.5, 20% PEG 3350 Resolution 2.63 Å R-free 0.269

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 8Z36 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CT7 Solution Structure of the IBR domain of the RING finger protein 31 protein Deposited 2005-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 779–851（73 aa） Fragment：IBR domain
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 220；Pressure ambient
NMR sample composition 1.55mM IBR domain U-13C,15N; 20mM d-Tris-HCl; 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZnCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
4DBG Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative Deposited 2012-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 480–636（157 aa） Fragment：Ub-associated domain, residues 480-636
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；15%(w/v) PEG6000, 0.1M KCl, 0.1M HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.71 Å R-free 0.253
4JUY Crystal structure of the PUB domain of E3 ubiquitin ligase RNF31 Deposited 2013-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–180（180 aa）
Chain B 1–180（180 aa）
Not recorded UNX UNKNOWN LIGAND × 40 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.8M K/Na tartrate tetrahydrate, 0.5% PEG MME 5000, 0.1 M BisTris, pH 8.5, vapor diffusion, hanging drop, temperature 291K
Resolution 2.40 Å R-free 0.258
4LJO Structure of an active ligase (HOIP)/ubiquitin transfer complex Deposited 2013-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 853–1072（220 aa） Fragment：E3 ligase HOIP catalytic core (unp residues 853-1072)
Not recorded ZN ZINC ION × 5 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1 M carboxylic acids, 0.1 M imidazole, MES, 30 % P550 MME_P20K, pH 6.5, vapour diffusion, temperature 293K, VAPOR DIFFUSION
Resolution 1.56 Å R-free 0.212
4LJP Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex Deposited 2013-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 853–1072（220 aa） Fragment：E3 ligase HOIP catalytic core (unp residues 853-1072)
Mutation：H889A ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M amino acids, 0.1 M imidazole, MES, 30 % P550 MME_P20K , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.15 Å R-free 0.216
4LJQ Crystal structure of the catalytic core of E3 ligase HOIP Deposited 2013-07-05 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 B 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.45 Å R-free 0.243
4LJQ Crystal structure of the catalytic core of E3 ligase HOIP Deposited 2013-07-05 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 A 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.45 Å R-free 0.243
4LJQ Crystal structure of the catalytic core of E3 ligase HOIP Deposited 2013-07-05 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 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.45 Å R-free 0.243
4LJQ Crystal structure of the catalytic core of E3 ligase HOIP Deposited 2013-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.45 Å R-free 0.243
4LJQ Crystal structure of the catalytic core of E3 ligase HOIP Deposited 2013-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Chain C 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.45 Å R-free 0.243
4LJQ Crystal structure of the catalytic core of E3 ligase HOIP Deposited 2013-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Chain D 853–1072（220 aa） Fragment：Catalytic domain (unp residues 853-1072)
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.45 Å R-free 0.243
4OWF Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain Deposited 2014-01-31 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 G 199–228（30 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Co-crystals were obtained after 6 days in 20% (w/v) PEG-3350 and 0.2 M DL-malic acid
Resolution 2.00 Å R-free 0.313
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 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 1–184（184 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 1–184（184 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain K 1–184（184 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 1–184（184 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 13 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain M 1–184（184 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 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 1–184（184 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 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 1–184（184 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–184（184 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–184（184 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–184（184 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–184（184 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–184（184 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYJ Structure of the apo HOIP PUB domain Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 1–184（184 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5
Resolution 3.00 Å R-free 0.255
4OYK Structure of HOIP PUB domain bound to OTULIN PIM Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3–179（177 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；295 K；32% PEG 6000, 1M LiCl, 100 mM Tris pH 8.4
Resolution 2.00 Å R-free 0.237
4OYK Structure of HOIP PUB domain bound to OTULIN PIM Deposited 2014-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 3–179（177 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；295 K；32% PEG 6000, 1M LiCl, 100 mM Tris pH 8.4
Resolution 2.00 Å R-free 0.237
4P09 Crystal structure of HOIP PUB domain Deposited 2014-02-20 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 1–179（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 8.5
Resolution 1.70 Å R-free 0.230
4P0A Crystal structure of HOIP PUB domain in complex with p97 PIM Deposited 2014-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–179（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 6.5
Resolution 2.30 Å R-free 0.249
4P0A Crystal structure of HOIP PUB domain in complex with p97 PIM Deposited 2014-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–179（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 6.5
Resolution 2.30 Å R-free 0.249
4P0B Crystal structure of HOIP PUB domain in complex with OTULIN PIM Deposited 2014-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–179（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 7.5
Resolution 2.70 Å R-free 0.270
4P0B Crystal structure of HOIP PUB domain in complex with OTULIN PIM Deposited 2014-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–179（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0,1M Tris, 20% 2-methyl-2,4-pentanediol, 15% Polyethyleneglycol 3350, pH 7.5
Resolution 2.70 Å R-free 0.270
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 696–1072（377 aa） Fragment：UNP residues 696-1072
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 696–1072（377 aa） Fragment：UNP residues 696-1072
Chain B 696–1072（377 aa） Fragment：UNP residues 696-1072
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 696–1072（377 aa） Fragment：UNP residues 696-1072
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5LJN Structure of the HOIP PUB domain bound to SPATA2 PIM peptide Deposited 2016-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 5–176（172 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.7-1.9 M (NH4)2SO4, 50 mM sodium cacodylate pH 6.4-7.0, 15 mM MgCl2 Protein:precipitant ratio; 1:2 200 nl drops
Resolution 2.70 Å R-free 0.281
5LJN Structure of the HOIP PUB domain bound to SPATA2 PIM peptide Deposited 2016-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–176（172 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.7-1.9 M (NH4)2SO4, 50 mM sodium cacodylate pH 6.4-7.0, 15 mM MgCl2 Protein:precipitant ratio; 1:2 200 nl drops
Resolution 2.70 Å R-free 0.281
5X0W Molecular mechanism for the binding between Sharpin and HOIP Deposited 2017-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 480–639（160 aa） Fragment：UNP residues 480-639
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；0.1 M HEPES (pH 7.3), 7% (w/v) PEG8000, 8% (v/v) ethylene glycerol
Resolution 3.00 Å R-free 0.302
5X0W Molecular mechanism for the binding between Sharpin and HOIP Deposited 2017-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 480–639（160 aa） Fragment：UNP residues 480-639
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；0.1 M HEPES (pH 7.3), 7% (w/v) PEG8000, 8% (v/v) ethylene glycerol
Resolution 3.00 Å R-free 0.302
5X0W Molecular mechanism for the binding between Sharpin and HOIP Deposited 2017-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 480–639（160 aa） Fragment：UNP residues 480-639
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；0.1 M HEPES (pH 7.3), 7% (w/v) PEG8000, 8% (v/v) ethylene glycerol
Resolution 3.00 Å R-free 0.302
5X0W Molecular mechanism for the binding between Sharpin and HOIP Deposited 2017-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 480–639（160 aa） Fragment：UNP residues 480-639
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；289 K；0.1 M HEPES (pH 7.3), 7% (w/v) PEG8000, 8% (v/v) ethylene glycerol
Resolution 3.00 Å R-free 0.302
6GZY HOIP-fragment5 complex Deposited 2018-07-05 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 853–1072（220 aa）
Not recorded FHH methyl 4-[(2-oxidanylidene-1,5,6,7-tetrahydrocyclopenta[b]pyridin-3-yl)carbonylamino]butanoate × 1 ZN ZINC ION × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 PGE TRIETHYLENE GLYCOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris HCl pH 8.5, 28% w/v PEG 4000, 0.2 M Li2SO4
Resolution 2.15 Å R-free 0.246
6GZY HOIP-fragment5 complex Deposited 2018-07-05 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 853–1072（220 aa）
Not recorded FHH methyl 4-[(2-oxidanylidene-1,5,6,7-tetrahydrocyclopenta[b]pyridin-3-yl)carbonylamino]butanoate × 1 ZN ZINC ION × 4 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris HCl pH 8.5, 28% w/v PEG 4000, 0.2 M Li2SO4
Resolution 2.15 Å R-free 0.246
6KC5 HOIP-HOIPIN1 complex Deposited 2019-06-27 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 B 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D5U 2-[3-(2-methoxyphenyl)-3-oxidanylidene-propyl]benzoic acid × 1 GOL GLYCEROL × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM HEPES-Na (pH 7.5), 200 mM NaCl, 25% PEG 3,350
Resolution 1.54 Å R-free 0.217
6KC6 HOIP-HOIPIN8 complex Deposited 2019-06-27 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 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D60 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；200 mM KCl, 20% PEG3,350
Resolution 2.12 Å R-free 0.267
6KC6 HOIP-HOIPIN8 complex Deposited 2019-06-27 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 C 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D60 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；200 mM KCl, 20% PEG3,350
Resolution 2.12 Å R-free 0.267
6KC6 HOIP-HOIPIN8 complex Deposited 2019-06-27 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 E 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D60 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；200 mM KCl, 20% PEG3,350
Resolution 2.12 Å R-free 0.267
6KC6 HOIP-HOIPIN8 complex Deposited 2019-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D60 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；200 mM KCl, 20% PEG3,350
Resolution 2.12 Å R-free 0.267
6KC6 HOIP-HOIPIN8 complex Deposited 2019-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D60 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；200 mM KCl, 20% PEG3,350
Resolution 2.12 Å R-free 0.267
6KC6 HOIP-HOIPIN8 complex Deposited 2019-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain K 853–1072（220 aa）
Not recorded ZN ZINC ION × 4 D60 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；200 mM KCl, 20% PEG3,350
Resolution 2.12 Å R-free 0.267
6SC5 dAb3/HOIP-RBR-Ligand2 Deposited 2019-07-23 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 697–1072（376 aa）
Not recorded L6B methyl 4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-3-enoate × 1 ZN ZINC ION × 8 SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Ammonium sulfate, sodium chloride, HEPES
Resolution 2.10 Å R-free 0.252
6SC6 dAb3/HOIP-RBR apo structure Deposited 2019-07-23 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 697–1072（376 aa）
Not recorded ZN ZINC ION × 8 SO4 SULFATE ION × 5 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Ammonium sulfate, sodium chloride, HEPES
Resolution 2.25 Å R-free 0.246
6SC7 dAb3/HOIP-RBR-Ligand3 Deposited 2019-07-23 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 697–1072（376 aa）
Not recorded L6H [2-[3-(cyclooct-4-en-1-yloxycarbonylamino)propylamino]-2-oxidanylidene-ethyl] (~{E})-4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-2-enoate × 1 ZN ZINC ION × 8 SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Ammonium sulfate, sodium chloride, HEPES
Resolution 2.56 Å R-free 0.267
6SC8 dAb3/HOIP-RBR-Ligand4 Deposited 2019-07-23 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 697–1072（376 aa）
Not recorded L6E [2-(methylamino)-2-oxidanylidene-ethyl] (~{E})-4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-2-enoate × 1 ZN ZINC ION × 8 SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Ammonium sulfate, sodium chloride, HEPES
Resolution 2.11 Å R-free 0.261
6SC9 dAb3/HOIP-RBR-HOIPIN-8 Deposited 2019-07-23 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 697–1072（376 aa）
Not recorded L68 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-prop-1-enyl]-4-(1-methylpyrazol-4-yl)benzoic acid × 1 ZN ZINC ION × 8 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Ammonium sulfate, sodium chloride, HEPES
Resolution 2.47 Å R-free 0.252
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 K 350–379（30 aa） Fragment：Residues 350-379
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
7UY2 Structure of RNF31 in complex with FP06649, a Helicon Polypeptide Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–179（179 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Resolution 2.51 Å R-free 0.270
7UY2 Structure of RNF31 in complex with FP06649, a Helicon Polypeptide Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–179（179 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Resolution 2.51 Å R-free 0.270
7UYJ Structure of RNF31 in complex with FP06652, a Helicon Polypeptide Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–179（179 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Amino Acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine),0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 30.0% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Resolution 2.32 Å R-free 0.274
7UYJ Structure of RNF31 in complex with FP06652, a Helicon Polypeptide Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–179（179 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Amino Acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine),0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 30.0% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Resolution 2.32 Å R-free 0.274
7UYK Structure of RNF31 in complex with FP06655, a Helicon Polypeptide Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 480–639（160 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；10% w/v glycerol, 20% w/v ethanol
Resolution 2.70 Å R-free 0.245
7UYK Structure of RNF31 in complex with FP06655, a Helicon Polypeptide Deposited 2022-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 480–639（160 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；10% w/v glycerol, 20% w/v ethanol
Resolution 2.70 Å R-free 0.245
7V8F Crystal structure of UBE2L3 bound to HOIP RING1 domain. Deposited 2021-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 697–793（97 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；289 K；2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(w/v) PEG 3,350.
Resolution 1.66 Å R-free 0.198
7V8G Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 697–793（97 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；289 K；2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(v/v) PEG 3,350
Resolution 2.75 Å R-free 0.278
7V8G Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 697–793（97 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；289 K；2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(v/v) PEG 3,350
Resolution 2.75 Å R-free 0.278
8Z30 Crystal structure of HOIP PUB domain in complex with tolfenamic acid complex Deposited 2024-04-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 4–179（176 aa）
Chain B 4–179（176 aa）
Chain C 4–179（176 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 3 TLF 2-[(3-chloro-2-methylphenyl)amino]benzoic acid × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20 mM Tris, 150 mM NaCl, pH 7.5, 10% w/v PEG1000, 10% w/v PEG8000
Resolution 2.30 Å R-free 0.242
9AZJ Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain E 351–379（29 aa） Fragment：HOIP NZF domain, residues 351-379
Chain G 351–379（29 aa） Fragment：HOIP NZF domain, residues 351-379
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.6；293 K；150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol
Resolution 3.32 Å R-free 0.285
9B0B Structure of Optineurin bound to HOIP NZF1 domain Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 350–379（30 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 5 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；3:1 (protein:mother liquor: 10% PEG 8K, 20% ethylene glycol, 0.1 M Tris/Bicine pH 8.5, 0.03 M MgCl2 and 0.03 M CaCl2. cryoprotected in mother liquor containing 10% glycerol
Resolution 1.70 Å R-free 0.222
9B0B Structure of Optineurin bound to HOIP NZF1 domain Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 350–379（30 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 5 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；3:1 (protein:mother liquor: 10% PEG 8K, 20% ethylene glycol, 0.1 M Tris/Bicine pH 8.5, 0.03 M MgCl2 and 0.03 M CaCl2. cryoprotected in mother liquor containing 10% glycerol
Resolution 1.70 Å R-free 0.222
9B0Z Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 350–379（30 aa）
Chain F 350–379（30 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol
Resolution 2.41 Å R-free 0.270
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 350–379（30 aa）
Chain H 350–379（30 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 350–379（30 aa）
Chain J 350–379（30 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9IIC Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain Deposited 2024-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 857–1071（215 aa） Fragment：RING2-LDD
Not recorded GOL GLYCEROL × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium citrate tribasic (pH 7.0), 20% w/v Polyethylene glycol 3350
Resolution 2.78 Å R-free 0.280
9IIC Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain Deposited 2024-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 857–1071（215 aa） Fragment：RING2-LDD
Not recorded GOL GLYCEROL × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium citrate tribasic (pH 7.0), 20% w/v Polyethylene glycol 3350
Resolution 2.78 Å R-free 0.280

35 other PDB entries and 74 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNF31_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–176； UniProt 4–179 Author chain B； PDBConstruct 1–176； UniProt 4–179 Author chain C； PDBConstruct 1–176； UniProt 4–179

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

SAXS scattering curve SAXS Profile

SAXS profile for 8z36

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8z36
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8z36
Deposition date deposition_date2024-04-14
Structure title titleCrystal structure of HOIP PUB domain in complex with sertraline complex
Keywords keywordsE3 ubiquitin-protein ligase HOIP, sertraline, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.54 Å
Radius of gyration Rg (electron density) rg_electron25.51 Å
Forward intensity I(0) i054889700.00
Molecular weight molecular_weight57532.0 kDa
Excluded volume excluded_volume72100 ų
Envelope volume envelope_volume89987 ų
Hydration-shell volume shell_volume29442 ų
Envelope diameter envelope_diameter88.4 Å
Shell Rg shell_rg32.65 Å
Envelope Rg envelope_rg25.45 Å
Shape Rg shape_rg25.53 Å
Total Rg total_rg26.26 Å
Total atoms total_atoms4068
Residues n_residues523
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax84.8 Å
Rg (real space) rg_real26.45 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real5.4890e+07
I(0) uncertainty (real space) i0_real_error6.8430e+05
Rg (reciprocal space) rg_reciprocal26.48 Å
I(0) (reciprocal space) i0_reciprocal54890000.0000
Solution quality estimate total_estimate0.9042
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.5 Å
Skewness Skewness skewness0.224
Kurtosis Kurtosis kurtosis-0.441
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11630000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)