3ivb

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

Method: X-RAY DIFFRACTION D_max: 52.2 Å Quality: GOOD

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

Speckle-type POZ protein

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–166	Fragment：UNP residues 28-166	Core histone macro-H2A.1 × 1 （O75367） ZN ZINC ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；10-20% PEG3350, 0.1 M Tris pH 7.6, 50 mM zinc acetate. Cryoprotection 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.247

Other States of the Same Protein in the Database

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

Other PDB	Difference from Current Entry 3IVB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CR2 Solution structure of N-terminal domain of speckle-type POZ protein Deposited 2005-05-20	Different construct 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 28–173（146 aa） Fragment：math domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.25mM math domain U-13C,15N; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
3HQI Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1 Deposited 2009-06-07	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 28–329（302 aa） Fragment：UNP residues 28-329 Chain B 28–329（302 aa） Fragment：UNP residues 28-329	Mutation：D140G Mutation：D140G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；pH 5.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.62 Å R-free 0.275
3HQL Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2 Deposited 2009-06-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa） Fragment：UNP residues 28-166	Mutation：D140G	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.66 Å R-free 0.258
3HQL Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2 Deposited 2009-06-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–166（139 aa） Fragment：UNP residues 28-166	Mutation：D140G	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.66 Å R-free 0.258
3HQM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 Deposited 2009-06-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa） Fragment：UNP residues 28-166	Mutation：D140G	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å R-free 0.218
3HQM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 Deposited 2009-06-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–166（139 aa） Fragment：UNP residues 28-166	Mutation：D140G	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å R-free 0.218
3HSV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2 Deposited 2009-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–166（139 aa） Chain B 28–166（139 aa）	Mutation：D140G Mutation：D140G	ZN ZINC ION × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.43 Å R-free 0.206
3HTM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box Deposited 2009-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 172–329（158 aa） Fragment：UNP residues 172-329 Chain B 172–329（158 aa） Fragment：UNP residues 172-329	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.256
3HTM Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box Deposited 2009-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 172–329（158 aa） Fragment：UNP residues 172-329 Chain D 172–329（158 aa） Fragment：UNP residues 172-329	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.256
3HU6 Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1 Deposited 2009-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 28–329（302 aa） Fragment：UNP residues 28-329 Chain B 28–329（302 aa） Fragment：UNP residues 28-329	Mutation：D140G Mutation：D140G	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.296
3IVQ Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2 Deposited 2009-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.279
3IVQ Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2 Deposited 2009-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.279
3IVV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-PucSBC1_pep1 Deposited 2009-09-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；22% PME 550, 0.1 M HEPES, Cryoprotection: 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.25 Å R-free 0.199
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319 Chain C 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 177–319（143 aa） Fragment：BTB domain from SPOP, unp residues 177-319	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.263
4HS2 Crystal Structure of the Human SPOP C-terminal Domain Deposited 2012-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 270–374（105 aa） Fragment：C-terminal domain (UNP residues 270-374)	Mutation：L273D, L282D, L285K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；26% PEG 1500, 7% isopropanol, 0.1M CaCl2, 0.1M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.53 Å R-free 0.151
4J8Z Crystal Structure of the Human SPOP BTB Domain Deposited 2013-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 169–374（206 aa） Fragment：SPOP BTB domain, UNP residues 178-374	Mutation：Y353E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.42 Å R-free 0.255
4J8Z Crystal Structure of the Human SPOP BTB Domain Deposited 2013-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 169–374（206 aa） Fragment：SPOP BTB domain, UNP residues 178-374	Mutation：Y353E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；32% PEG3350, 17% isopropanol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.42 Å R-free 0.255
4O1V SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer Deposited 2013-12-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa） Fragment：MATH domain (UNP residues 28-166)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris, 100 mM sodium malonate, 36% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.221
6F8F Co-crystal structure of SPOP MATH domain and human Pdx1 fragment Deposited 2017-12-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES pH 6.5, 10% (w/v) PEG6000 (final pH 7.0)	Resolution 2.00 Å R-free 0.274
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 28–166（139 aa） Chain B 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000	Resolution 2.03 Å R-free 0.262
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–166（139 aa） Chain D 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000	Resolution 2.03 Å R-free 0.262
6F8G Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment Deposited 2017-12-13	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 C 28–166（139 aa） Chain D 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000	Resolution 2.03 Å R-free 0.262
6I41 Co-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment Deposited 2018-11-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；100 mM Tris pH 8.5, 200 mM NaCl, 25% (w/v) PEG3350	Resolution 1.90 Å R-free 0.238
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Mutation：E47K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350	Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–166（139 aa）	Mutation：E47K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350	Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 28–166（139 aa）	Mutation：E47K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350	Resolution 1.81 Å R-free 0.227
6I5P Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment Deposited 2018-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 28–166（139 aa）	Mutation：E47K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350	Resolution 1.81 Å R-free 0.227
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Mutation：M117V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350	Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–166（139 aa）	Mutation：M117V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350	Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 28–166（139 aa）	Mutation：M117V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350	Resolution 1.85 Å R-free 0.237
6I68 Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment Deposited 2018-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 28–166（139 aa）	Mutation：M117V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350	Resolution 1.85 Å R-free 0.237
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 28–166（139 aa） Chain E 28–166（139 aa）	Mutation：D140N Mutation：D140N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000	Resolution 2.20 Å R-free 0.234
6I7A Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment Deposited 2018-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–166（139 aa） Chain G 28–166（139 aa）	Mutation：D140N Mutation：D140N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000	Resolution 2.20 Å R-free 0.234
7D3D Crystal structure of SPOP bound with a peptide Deposited 2020-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa） Fragment：UNP residues 28-166	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350	Resolution 1.45 Å R-free 0.189
7D3D Crystal structure of SPOP bound with a peptide Deposited 2020-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–166（139 aa） Fragment：UNP residues 28-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350	Resolution 1.45 Å R-free 0.189
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–166（138 aa） Fragment：MATH domain	Mutation：D140G	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350	Resolution 3.40 Å R-free 0.241
7KLZ Structure of SPOP MATH domain in complex with a Geminin peptide Deposited 2020-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–166（138 aa） Fragment：MATH domain	Mutation：D140G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；One microliter of the protein complex in 20 mM Tris-HCl, pH 7.6, 50 mM NaCl and 5 mM dithiothreitol was mixed with on microliter of 0.2 M ammonium citrate dibasic and 20% (W/V) PEG 3350	Resolution 3.40 Å R-free 0.241
7LIN X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–166（138 aa） Fragment：MATH domain	Mutation：D140G	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4	Resolution 1.44 Å R-free 0.186
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–166（138 aa） Fragment：MATH domain	Mutation：S119D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.	Resolution 3.01 Å R-free 0.277
7LIO X-ray structure of SPOP MATH domain (S119D) in complex with a 53BP1 peptide Deposited 2021-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–166（138 aa） Fragment：MATH domain	Mutation：S119D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；SPOP MATH (S119D) was at a concentration of 20 mg/ml with a 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml of 2 M (NH4)2SO4.	Resolution 3.01 Å R-free 0.277
7LIP X-ray structure of SPOP MATH domain (D140G) Deposited 2021-01-27	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 29–166（138 aa） Fragment：MATH domain	Mutation：D140G	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4. Two ul of the protein at 24 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT was mixed with 2 ul of the reservoir solution. The reservoir solution was 0.5 ml.	Resolution 1.48 Å R-free 0.205
7LIQ X-ray structure of SPOP MATH domain (S119A) Deposited 2021-01-27	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 29–166（138 aa） Fragment：MATH domain	Mutation：S119A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Crystals were grown by the hanging drop method, mixing 2 ul of the SPOP MATH S119A at 20 mg/ml in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.2 M (NH4)2SO4, 0.1 M BIS-Tris, pH 6.5, 25% (w/v) PEG 3,350).	Resolution 1.98 Å R-free 0.225
8DWS Full-length E47K SPOP Deposited 2022-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–374（374 aa） Chain B 1–374（374 aa） Chain D 1–374（374 aa） Chain E 1–374（374 aa） Chain F 1–374（374 aa） Chain G 1–374（374 aa） Chain H 1–374（374 aa）	Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K Mutation：E47K	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
8DWT SPOP W22R Form 2 Deposited 2022-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 2–374（373 aa） Chain B 2–374（373 aa） Chain C 2–374（373 aa） Chain D 2–374（373 aa） Chain E 2–374（373 aa） Chain F 2–374（373 aa） Chain G 2–374（373 aa） Chain H 2–374（373 aa） Chain I 2–374（373 aa） Chain J 2–374（373 aa） Chain K 2–374（373 aa） Chain L 2–374（373 aa）	Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.20 Å
8DWU SPOP W22R Form 1 Deposited 2022-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 1–374（374 aa） Chain B 1–374（374 aa） Chain C 1–374（374 aa） Chain D 1–374（374 aa） Chain E 1–374（374 aa） Chain F 1–374（374 aa） Chain H 1–374（374 aa） Chain I 1–374（374 aa） Chain J 1–374（374 aa）	Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R Mutation：W22R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8DWV Full-length wild type SPOP Deposited 2022-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 400 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9HFV MyD88 peptide_2 bound to SPOP MATH domain Deposited 2024-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MOPS/HEPES-Na pH 7.5	Resolution 1.45 Å R-free 0.214
9HGG SETD2 peptide bound to SPOP MATH domain Deposited 2024-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–166（139 aa）	Not recorded	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5	Resolution 1.90 Å R-free 0.256
9OUT SPOP double donut locally refined MATH domains Deposited 2025-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–374（374 aa） Chain B 1–374（374 aa） Chain C 1–374（374 aa） Chain D 1–374（374 aa） Chain E 1–374（374 aa） Chain F 1–374（374 aa） Chain G 1–374（374 aa） Chain H 1–374（374 aa） Chain I 1–374（374 aa） Chain J 1–374（374 aa） Chain K 1–374（374 aa） Chain L 1–374（374 aa） Chain M 1–374（374 aa） Chain N 1–374（374 aa） Chain P 1–374（374 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9OUU SPOP double donut locally refined MATH domains Deposited 2025-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa） Chain K 1–373（373 aa） Chain L 1–373（373 aa） Chain M 1–373（373 aa） Chain N 1–373（373 aa） Chain P 1–373（373 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9OUW SPOP double donut locally refined MATH domains Deposited 2025-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain D 1–373（373 aa） Chain F 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa） Chain L 1–373（373 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

34 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPOP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–145； UniProt 28–166

Core histone macro-H2A.1

OrganismNot specified

UniProt O75367

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 167–181	Not recorded	Speckle-type POZ protein × 1 （O43791） ZN ZINC ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；10-20% PEG3350, 0.1 M Tris pH 7.6, 50 mM zinc acetate. Cryoprotection 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.247

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3IVB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U35 Crystal structure of the nucleosome core particle containing the histone domain of macroH2A Deposited 2004-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–120（120 aa） Chain G 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；potassium chloride, manganese chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.00 Å R-free 0.260
1ZR5 Crystal structure of the macro-domain of human core histone variant macroH2A1.2 Deposited 2005-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 161–372（212 aa） Fragment：non-histone macro-domain (Residues: 161-372)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG 5000MME 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.92 Å R-free 0.277
1ZR5 Crystal structure of the macro-domain of human core histone variant macroH2A1.2 Deposited 2005-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 161–372（212 aa） Fragment：non-histone macro-domain (Residues: 161-372)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG 5000MME 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.92 Å R-free 0.277
2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–119（119 aa） Fragment：residues 0-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.90 Å R-free 0.269
3HSV Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2 Deposited 2009-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 171–186（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.43 Å R-free 0.206
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 181–366（186 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 181–366（186 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 181–366（186 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 181–366（186 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5LNC Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 182–366（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8.75% PEG 6000, 2.75M NaCl	Resolution 3.29 Å R-free 0.302
5LNC Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 182–366（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8.75% PEG 6000, 2.75M NaCl	Resolution 3.29 Å R-free 0.302

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H2AY_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–15； UniProt 167–181

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	3ivb
Deposition date deposition_date	2009-08-31
Structure title title	Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1
Keywords keywords	;Protein Binding/Hydrolase, Nucleus, Ubl conjugation pathway, Alternative splicing, Chromatin regulator, Chromosomal protein, DNA-binding, Isopeptide bond, Methylation, Nucleosome core, Phosphoprotein, Ubl conjugation, protein binding, ligase ;; protein binding, 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	16.71 Å
Radius of gyration Rg (electron density) rg_electron	15.12 Å
Forward intensity I(0) i0	5657280.00
Molecular weight molecular_weight	17047.0 kDa
Excluded volume excluded_volume	21181 Å³
Envelope volume envelope_volume	23938 Å³
Hydration-shell volume shell_volume	13485 Å³
Envelope diameter envelope_diameter	50.4 Å
Shell Rg shell_rg	20.84 Å
Envelope Rg envelope_rg	15.49 Å
Shape Rg shape_rg	14.99 Å
Total Rg total_rg	16.51 Å
Total atoms total_atoms	1180
Residues n_residues	148
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	52.2 Å
Rg (real space) rg_real	16.63 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	5.6570e+06
I(0) uncertainty (real space) i0_real_error	6.4070e+04
Rg (reciprocal space) rg_reciprocal	16.64 Å
I(0) (reciprocal space) i0_reciprocal	5657000.0000
Solution quality estimate total_estimate	0.8989
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.5 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	812000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Speckle-type POZ protein
Molecular weight formula_weight	16544.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1307

GSGGSGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD

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 polymer

Description description	Core histone macro-H2A.1
Molecular weight formula_weight	1422.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

KAASADSTTEGTPAD

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ivba_
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

CATH v4.4 (1 domains)

Domain ID domain_id	3ivbA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

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8. Citations (1)

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Unit-cell length a length_a	44.021 Å
Unit-cell length b length_b	44.021 Å
Unit-cell length c length_c	266.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	37.740 Å
R factor r_factor	0.2196
R_work r_work	0.2183
R_free r_free	0.2473

fit	/app/data/saxs_computation/iv/3ivb/3ivb.fit
pddf	/app/data/pr_computation/iv/3ivb/3ivb.pr.out
profile	/app/data/saxs_computation/iv/3ivb/3ivb.dat

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

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

Speckle-type POZ protein

State in the Current Structure

Other States of the Same Protein in the Database

Core histone macro-H2A.1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)