4oyj

Structure of the apo HOIP PUB domain

Method: X-RAY DIFFRACTION D_max: 135.0 Å Quality: GOOD

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

E3 ubiquitin-protein ligase RNF31

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–184	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
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 1–184	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
11	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain K； UniProt 1–184	Not recorded	No other associated polymer	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
12	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain L； UniProt 1–184	Not recorded	No other associated polymer	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
13	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain M； UniProt 1–184	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–184	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–184	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–184	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–184	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–184	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
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–184	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
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–184	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
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 1–184	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

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 4OYJ	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 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 oligomeric state 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 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 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 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 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 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 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
4OYK Structure of HOIP PUB domain bound to OTULIN PIM Deposited 2014-02-12	Different construct 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 construct Different mutation/modification Different oligomeric state 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
8Z36 Crystal structure of HOIP PUB domain in complex with sertraline complex Deposited 2024-04-14	Different construct Different mutation/modification Different oligomeric state 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	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
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 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 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 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 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 62 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 3–186； UniProt 1–184 Author chain B； PDBConstruct 3–186； UniProt 1–184 Author chain C； PDBConstruct 3–186； UniProt 1–184 Author chain D； PDBConstruct 3–186； UniProt 1–184 Author chain E； PDBConstruct 3–186； UniProt 1–184 Author chain F； PDBConstruct 3–186； UniProt 1–184 Author chain G； PDBConstruct 3–186； UniProt 1–184 Author chain H； PDBConstruct 3–186； UniProt 1–184 Author chain I； PDBConstruct 3–186； UniProt 1–184 Author chain J； PDBConstruct 3–186； UniProt 1–184 Author chain K； PDBConstruct 3–186； UniProt 1–184 Author chain L； PDBConstruct 3–186； UniProt 1–184 Author chain M； PDBConstruct 3–186； UniProt 1–184

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	4oyj
Deposition date deposition_date	2014-02-12
Structure title title	Structure of the apo HOIP PUB domain
Keywords keywords	E3 ubiquitin ligase, PUB domain, LIGASE; LIGASE
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	44.13 Å
Radius of gyration Rg (electron density) rg_electron	43.45 Å
Forward intensity I(0) i0	1055530000.00
Molecular weight molecular_weight	260890.0 kDa
Excluded volume excluded_volume	324030 Å³
Envelope volume envelope_volume	463950 Å³
Hydration-shell volume shell_volume	86148 Å³
Envelope diameter envelope_diameter	137.7 Å
Shell Rg shell_rg	51.06 Å
Envelope Rg envelope_rg	42.24 Å
Shape Rg shape_rg	43.46 Å
Total Rg total_rg	43.75 Å
Total atoms total_atoms	18383
Residues n_residues	2333
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	135.0 Å
Rg (real space) rg_real	43.84 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.0560e+09
I(0) uncertainty (real space) i0_real_error	1.6990e+07
Rg (reciprocal space) rg_reciprocal	44.13 Å
I(0) (reciprocal space) i0_reciprocal	1056000000.0000
Solution quality estimate total_estimate	0.8924
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	56.2 Å
Skewness Skewness skewness	0.069
Kurtosis Kurtosis kurtosis	-0.535
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	113000000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.834

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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	E3 ubiquitin-protein ligase RNF31
Molecular weight formula_weight	21101.7 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M
Atom count atom_count	18399

GPMPGEEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHGEPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYGYTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLLQNTHPRQQALEQLLEDKVED

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 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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7. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	4oyjA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

Domain ID domain_id	4oyjM00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	2190 —

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8. Citations (1)

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Unit-cell length a length_a	155.190 Å
Unit-cell length b length_b	99.540 Å
Unit-cell length c length_c	173.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	52

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	62.605 Å
R factor r_factor	0.2094
R_work r_work	0.2070
R_free r_free	0.2545

fit	/app/data/saxs_computation/oy/4oyj/4oyj.fit
pddf	/app/data/pr_computation/oy/4oyj/4oyj.pr.out
profile	/app/data/saxs_computation/oy/4oyj/4oyj.dat