5jh5

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

Method: X-RAY DIFFRACTION D_max: 115.8 Å Quality: GOOD

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

Lysine-specific demethylase 2B

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1059–1336	Fragment：RESIDUES 1059-1336 Non-standard monomer：Yes (specific site not provided by mmCIF)	S-phase kinase-associated protein 1 × 1 （P63208） Polycomb group RING finger protein 1 × 1 （Q9BSM1） BCL-6 corepressor-like protein 1 × 1 （Q5H9F3）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl	Resolution 2.55 Å R-free 0.257

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 5JH5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4O64 Zinc fingers of KDM2B Deposited 2013-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 607–723（117 aa） Fragment：UNP Residues 607-723	Not recorded	ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 8.5；291 K；25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K	Resolution 2.13 Å R-free 0.220
4O64 Zinc fingers of KDM2B Deposited 2013-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 607–723（117 aa） Fragment：UNP Residues 607-723	Not recorded	ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 8.5；291 K；25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K	Resolution 2.13 Å R-free 0.220
4O64 Zinc fingers of KDM2B Deposited 2013-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 607–723（117 aa） Fragment：UNP Residues 607-723	Not recorded	ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop；pH 8.5；291 K；25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K	Resolution 2.13 Å R-free 0.220
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 991–1035（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000	Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 991–1035（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000	Resolution 2.66 Å R-free 0.263

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–281； UniProt 1059–1336

S-phase kinase-associated protein 1

Homo sapiens

UniProt P63208

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 2–163	Fragment：Residues 2-163 Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase 2B × 1 （Q8NHM5） Polycomb group RING finger protein 1 × 1 （Q9BSM1） BCL-6 corepressor-like protein 1 × 1 （Q5H9F3）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl	Resolution 2.55 Å R-free 0.257

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5JH5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	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 B 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	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 D 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	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 F 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	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 H 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.314
1FS1 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX Deposited 2000-09-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–147（147 aa） Fragment：RESIDUES 1-147 Chain D 1–147（147 aa） Fragment：RESIDUES 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；PEG 1500, sodium acetate, ammonium acetate, DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.274
1FS2 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX Deposited 2000-09-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–146（146 aa） Fragment：RESIDUES 1-37; 43-147 Chain D 1–146（146 aa） Fragment：RESIDUES 1-37; 43-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.287
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–139（139 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.331
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 1–139（139 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.331
1P22 Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase Deposited 2003-04-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG4000, sodium citrate, Bis-Tris Propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.95 Å R-free 0.286
29HG Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10088 Deposited 2026-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–163（163 aa）	Not recorded	A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
29HH Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1 Deposited 2026-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 1–163（163 aa）	Not recorded	A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
29HI Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667 Deposited 2026-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–163（163 aa）	Not recorded	A1J21 4-[[cyclopropyl-[(~{Z})-2-methyl-4-(5-oxidanylidene-2~{H}-1,4-oxazin-3-yl)but-3-enoyl]amino]methyl]-~{N}-[3-[2-[[4-(hydroxymethyl)phenyl]carbonyl-methyl-amino]ethyl]phenyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–159（159 aa）	Mutation：P1A	PO4 PHOSPHATE ION × 3 BEN BENZAMIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–159（159 aa）	Mutation：P1A	PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–159（159 aa）	Mutation：P1A	PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.242
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–159（159 aa）	Not recorded	BEN BENZAMIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24	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 1–159（159 aa）	Not recorded	BEN BENZAMIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–159（159 aa）	Not recorded	BEN BENZAMIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.221
2E31 Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase Deposited 2006-11-20	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 B 0–162（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.291
2E32 Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase Deposited 2006-11-20	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 B 0–162（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.52 Å R-free 0.299
2E32 Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase Deposited 2006-11-20	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 D 0–162（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.52 Å R-free 0.299
2OVP Structure of the Skp1-Fbw7 complex Deposited 2007-02-14	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 1–163（163 aa） Fragment：residues 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES-Na, 1.2 M Li2SO4, 7.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.90 Å R-free 0.268
2OVP Structure of the Skp1-Fbw7 complex Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–163（163 aa） Fragment：residues 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES-Na, 1.2 M Li2SO4, 7.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.90 Å R-free 0.268
2OVQ Structure of the Skp1-Fbw7-CyclinEdegC complex Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–163（163 aa） Fragment：residues 1-147	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；294 K；0.1 M Bicine, 1.4 M Li2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.266
2OVQ Structure of the Skp1-Fbw7-CyclinEdegC complex Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–163（163 aa） Fragment：residues 1-147	Not recorded	SO4 SULFATE ION × 32	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；294 K；0.1 M Bicine, 1.4 M Li2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.266
2OVR Structure of the Skp1-Fbw7-CyclinEdegN complex Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–163（163 aa） Fragment：residues 1-147	Not recorded	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M Hepes-Na, 1.12 M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.50 Å R-free 0.251
3L2O Structure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase Deposited 2009-12-15	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 1–163（163 aa）	Mutation：deletion: 38-43, 70-81; P2A; insertion: GGSG between 69 and 82	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.5-2 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.80 Å R-free 0.295
3L2O Structure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase Deposited 2009-12-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–163（163 aa）	Mutation：deletion: 38-43, 70-81; P2A; insertion: GGSG between 69 and 82	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.5-2 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.80 Å R-free 0.295
3WSO Crystal structure of the Skp1-FBG3 complex Deposited 2014-03-18	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 B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；8% 2-propanol, 16% PEG4000, 0.1M Na PIPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.60 Å R-free 0.266
4I6J A ubiquitin ligase-substrate complex Deposited 2012-11-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.2M ammonium citrate, 13-14% PEG3350 7% Acetonitrile, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.265
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–69（69 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ; Chain A 82–163（82 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol	Resolution 2.50 Å R-free 0.240
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–69（69 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ; Chain D 82–163（82 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol	Resolution 2.50 Å R-free 0.240
5K35 Structure of the Legionella effector, AnkB, in complex with human Skp1 Deposited 2016-05-19	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 B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME	Resolution 2.85 Å R-free 0.275
5V4B Crystal structure of the Skp1-FBXW7-DISC1 complex Deposited 2017-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–69（69 aa） Chain A 82–163（82 aa）	Not recorded	SO4 SULFATE ION × 9 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277.15 K；100 mM Hepes, 1.2M lithium sulfate	Resolution 2.60 Å R-free 0.219
5V4B Crystal structure of the Skp1-FBXW7-DISC1 complex Deposited 2017-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–69（69 aa） Chain A 82–163（82 aa）	Not recorded	SO4 SULFATE ION × 36 IMD IMIDAZOLE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277.15 K；100 mM Hepes, 1.2M lithium sulfate	Resolution 2.60 Å R-free 0.219
5VZT Crystal structure of the Skp1-FBXO31 complex Deposited 2017-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–163（163 aa）	Mutation：P2A	ZN ZINC ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2	Resolution 2.70 Å R-free 0.242
5VZT Crystal structure of the Skp1-FBXO31 complex Deposited 2017-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–163（163 aa）	Mutation：P2A	ZN ZINC ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2	Resolution 2.70 Å R-free 0.242
5VZU Crystal structure of the Skp1-FBXO31-cyclin D1 complex Deposited 2017-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–163（163 aa）	Mutation：P2A	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2	Resolution 2.70 Å R-free 0.233
5VZU Crystal structure of the Skp1-FBXO31-cyclin D1 complex Deposited 2017-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–163（163 aa）	Mutation：P2A	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2	Resolution 2.70 Å R-free 0.233
5XYL Solution Structure of Skp1 from Homo sapiens Deposited 2017-07-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–163（163 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000	Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000	Resolution 2.66 Å R-free 0.263
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500	Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500	Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500	Resolution 2.61 Å R-free 0.294
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350	Resolution 3.27 Å R-free 0.317
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350	Resolution 3.27 Å R-free 0.317
6M90 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–163（162 aa）	Not recorded	J91 2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.05 Å R-free 0.212
6M91 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–163（162 aa）	Not recorded	J97 3-({4-[(2,6-dichlorophenyl)sulfanyl]-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl}amino)benzoic acid × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.40 Å R-free 0.216
6M92 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–163（162 aa）	Not recorded	J8V 3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.35 Å R-free 0.221
6M93 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–163（162 aa）	Not recorded	J8Y 2-oxo-N-[3-(1H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5	Resolution 2.50 Å R-free 0.230
6M94 Monophosphorylated pSer33 b-Catenin peptide bound to b-TrCP/Skp1 Complex Deposited 2018-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–163（162 aa）	Not recorded	PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH5.5	Resolution 2.70 Å R-free 0.238
6O60 Crystal structure of GGTase3-FBXL2-SKP1 complex Deposited 2019-03-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–163（163 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH6.0, 20%-22% (v/v) PEG 400	Resolution 2.50 Å R-free 0.247
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
6VCD Cryo-EM structure of IRP2-FBXL5-SKP1 complex Deposited 2019-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–163（163 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6W66 The structure of the F64A, S172A mutant Keap1-BTB domain in complex with SKP1-FBXL17 Deposited 2020-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；well solution 37.5 ul of 50 mM MgCl2, 100 mM HEPES pH 7.5, 30% (v/v) PEG MME 550 (E7 Hampton Index) + 12.5ul H2O mixed 1:1 with complex at 15mg/ml in 150 mM NaCl, 25 mM Tris/HCl pH 8.0	Resolution 3.21 Å R-free 0.290
6WCQ Structure of a substrate-bound DQC ubiquitin ligase Deposited 2020-03-31	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 8.50 Å
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–163（163 aa）	Not recorded	GOL GLYCEROL × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K	Resolution 2.50 Å R-free 0.251
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–163（163 aa）	Not recorded	GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K	Resolution 2.50 Å R-free 0.251
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–163（163 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K	Resolution 2.50 Å R-free 0.251
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
7B5R Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 Deposited 2020-12-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain S 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7T1Y Structure of the Fbw7-Skp1-MycCdegron complex Deposited 2021-12-02	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 2–163（162 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298.15 K；0.1 M Bicine pH6.5, 1.6 M Li2SO4	Resolution 2.55 Å R-free 0.268
7T1Z Structure of the Fbw7-Skp1-MycNdegron complex Deposited 2021-12-02	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 2–163（162 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298.15 K；0.1 M Bicine pH6.5, 1.6 M Li2SO4	Resolution 2.77 Å R-free 0.248
7Z8B Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation Deposited 2022-03-17	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7Z8T CAND1-SCF-SKP2 CAND1 engaged SCF rocked Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7Z8V CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7ZBW CAND1-SCF-SKP2 CAND1 rolling-2 SCF engaged Deposited 2022-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7ZBZ CAND1 delhairpin-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2022-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8BYA Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex Deposited 2022-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
8BYL Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex Deposited 2022-12-13	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8CDJ CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged Deposited 2023-01-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8CDK CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2023-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–163（163 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8S7D Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution Deposited 2024-02-29	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–163（163 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
8S7E Cryo-EM structure of SKP1-FBXO22 Deposited 2024-02-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–163（162 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8UA6 Cryo-EM Structure of SCF-FBOX22-BACH1BTB Deposited 2023-09-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8UBT Structure of SCF-FBXL17-BACH1BTB E3 ligase complex Deposited 2023-09-24	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–163（163 aa） Fragment：BTB domain (UNP residues 7-128)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8UBU Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation Deposited 2023-09-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain C 1–163（163 aa） Chain G 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
9CB3 E2F1-Cyclin F Interface Deposited 2024-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–163（163 aa） Fragment：BTB domain (UNP residues 7-128)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9JKB Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex Deposited 2024-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9KBD Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex Deposited 2024-10-30	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9KBF Cryo-EM structure of the SKP1-FBXO3 complex Deposited 2024-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain L 1–163（163 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain L 1–163（163 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric	Chain L 1–163（163 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain L 1–163（163 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain L 1–163（163 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9XZJ Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure) Deposited 2025-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric	Chain S 1–163（163 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9XZL Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (body structure) Deposited 2025-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain S 1–163（163 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

71 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SKP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–162； UniProt 2–163

Polycomb group RING finger protein 1

Homo sapiens

UniProt Q9BSM1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 150–255	Fragment：RESIDUES 150-255 Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase 2B × 1 （Q8NHM5） S-phase kinase-associated protein 1 × 1 （P63208） BCL-6 corepressor-like protein 1 × 1 （Q5H9F3）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl	Resolution 2.55 Å R-free 0.257

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5JH5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4HPL PCGF1 Ub fold (RAWUL)/BCOR PUFD Complex Deposited 2012-10-24	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 B 167–255（89 aa） Fragment：UNP residues 167-255	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；50 mM MES, 8.5% polyethylene glycol (PEG) 8000, 300 mM sodium bromide, 10% ethylene glycol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.261
4HPM PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex Deposited 2012-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 167–255（89 aa） Fragment：UNP residues 167-255	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；100 mM sodium citrate, 19% polyethylene glycol (PEG) 1500, 100 mM dibasic sodium phosphate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.247
4HPM PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex Deposited 2012-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 167–255（89 aa） Fragment：UNP residues 167-255	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；100 mM sodium citrate, 19% polyethylene glycol (PEG) 1500, 100 mM dibasic sodium phosphate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.247
8HCU Crystal structure of BCOR/PCGF1/KDM2B complex Deposited 2022-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 151–255（105 aa）	Not recorded	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.2；293 K；0.1M magnesium acetate, 0.1M sodium citrate pH6.2, 4% PEG5000MME	Resolution 2.20 Å R-free 0.238
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain M 1–259（259 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.20 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCGF1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–109； UniProt 150–255

BCL-6 corepressor-like protein 1

Homo sapiens

UniProt Q5H9F3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1594–1711	Fragment：RESIDUES 1594-1711 Non-standard monomer：Yes (specific site not provided by mmCIF)	Lysine-specific demethylase 2B × 1 （Q8NHM5） S-phase kinase-associated protein 1 × 1 （P63208） Polycomb group RING finger protein 1 × 1 （Q9BSM1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl	Resolution 2.55 Å R-free 0.257

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5JH5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4HPM PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex Deposited 2012-10-24	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 1594–1711（118 aa） Fragment：UNP residues 1594-1711	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；100 mM sodium citrate, 19% polyethylene glycol (PEG) 1500, 100 mM dibasic sodium phosphate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.247
4HPM PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex Deposited 2012-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1594–1711（118 aa） Fragment：UNP residues 1594-1711	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；100 mM sodium citrate, 19% polyethylene glycol (PEG) 1500, 100 mM dibasic sodium phosphate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.247

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

View Construct and Data Evidence

UniProt name	BCORL_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 5–122； UniProt 1594–1711

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	5jh5
Deposition date deposition_date	2016-04-20
Structure title title	Structural Basis for the Hierarchical Assembly of the Core of PRC1.1
Keywords keywords	gene repression, complex, transcription regulation, transcription repressor, METAL BINDING PROTEIN-TRANSCRIPTION complex; METAL BINDING PROTEIN/TRANSCRIPTION
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	30.95 Å
Radius of gyration Rg (electron density) rg_electron	30.82 Å
Forward intensity I(0) i0	83050700.00
Molecular weight molecular_weight	71348.0 kDa
Excluded volume excluded_volume	88905 Å³
Envelope volume envelope_volume	115150 Å³
Hydration-shell volume shell_volume	32236 Å³
Envelope diameter envelope_diameter	119.4 Å
Shell Rg shell_rg	36.54 Å
Envelope Rg envelope_rg	30.72 Å
Shape Rg shape_rg	30.82 Å
Total Rg total_rg	31.34 Å
Total atoms total_atoms	4951
Residues n_residues	594
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	115.8 Å
Rg (real space) rg_real	31.03 Å
Rg uncertainty (real space) rg_real_error	1.37 Å
I(0) (real space) i0_real	8.3050e+07
I(0) uncertainty (real space) i0_real_error	1.5510e+06
Rg (reciprocal space) rg_reciprocal	31.00 Å
I(0) (reciprocal space) i0_reciprocal	83050000.0000
Solution quality estimate total_estimate	0.8273
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.6 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.197
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24440000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.681; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.716; 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	Lysine-specific demethylase 2B
Molecular weight formula_weight	32494.6 kDa
EC 编号 ec_number	1.14.11.27
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	5015

GTRDGAAHVMHREVWMAVFSYLSHQDLCVCMRVCRTWNRWCCDKRLWTRIDLNHCKSITPLMLSGIIRRQPVSLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTDNRPGQMDNRSKLRNIVELRLAGLDITDASLRLIIRHMPLLSKLHLSYCNHVTDQSINLLTAVGTTTRDSLTEINLSDCNKVTDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSVSVQFGQVEEKLLQKLS

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	S-phase kinase-associated protein 1
Molecular weight formula_weight	18689.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Polycomb group RING finger protein 1
Molecular weight formula_weight	13205.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GTRLPFSSFDHSKAHYYRYDEQLNLCLERLSSGKDKNKSVLQNKYVRCSVRAEVRHLRRVLCHRLMLNPQHVQLLFDNEVLPDHMTMKQIWLSRWFGKPSPLLLQYSVK

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 4 Entity 4 polymer

Description description	BCL-6 corepressor-like protein 1
Molecular weight formula_weight	14164.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

METRDDFMFELSDKPLLPCYNLQVSVSRGPCNWFLFSDVLKRLKLSSRIFQARFPHFEITTMPKAEFYRQVASSQLLTPAERPGGLDDRSPPGSSETVELVRYEPDLLRLLGSEVEFQSCNS

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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5jh5b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.0 — automated matches

Domain ID domain_id	d5jh5b2
Class class	a — All alpha proteins
Fold Fold fold	a.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
Family Family family	a.157.1.1 — Skp1 dimerisation domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	5jh5B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	5jh5C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	70.049 Å
Unit-cell length b length_b	73.796 Å
Unit-cell length c length_c	123.014 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	63.282 Å
R factor r_factor	0.2110
R_work r_work	0.2062
R_free r_free	0.2573

fit	/app/data/saxs_computation/jh/5jh5/5jh5.fit
pddf	/app/data/pr_computation/jh/5jh5/5jh5.pr.out
profile	/app/data/saxs_computation/jh/5jh5/5jh5.dat

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

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

Lysine-specific demethylase 2B

State in the Current Structure

Other States of the Same Protein in the Database

S-phase kinase-associated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Polycomb group RING finger protein 1

State in the Current Structure

Other States of the Same Protein in the Database

BCL-6 corepressor-like protein 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

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)