9sdy

Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2

Method: ELECTRON MICROSCOPY D_max: 147.7 Å Quality: GOOD

▼

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

RING-box protein 2

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 R； UniProt 1–113	Not recorded	L3A2-1 × 1 Cullin-5 × 1 （Q93034） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.06 Å

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 9SDY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ECL Solution Structure of the RING domain of the human RING-box protein 2 Deposited 2007-02-13	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 40–113（74 aa） Fragment：RING domain	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1.11mM RING domain U-13C,15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZNCl2; 1.0mM IDA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
7ONI Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2* Deposited 2021-05-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 5–113（109 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain K 1–113（113 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9OMA Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1) Deposited 2025-05-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–113（113 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–113（113 aa）	Not recorded	ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.97 Å
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain R 5–113（109 aa）	Mutation：N-terminal residues 1-4 deleted	FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å

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

View Construct and Data Evidence

UniProt name	RBX2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 1–113； UniProt 1–113

Cullin-5

Homo sapiens

UniProt Q93034

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 1–780	Not recorded	L3A2-1 × 1 RING-box protein 2 × 1 （Q9UBF6） E3 ubiquitin-protein ligase ARIH2 × 1 （O95376） ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9SDY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DPL Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation. Deposited 2008-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 401–780（380 aa） Fragment：Residues 401-780	Mutation：L407E, L439K, V440K	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；277 K；2% PEG 3350, 0.1M HEPES, 0.2M L-proline, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.277
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09	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 401–780（380 aa） Fragment：Cullin-5 residues 401-780	Mutation：L407E, L439K, V440K Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 401–780（380 aa） Fragment：Cullin-5 residues 401-780	Mutation：L407E, L439K, V440K Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 401–780（380 aa） Fragment：Cullin-5 residues 401-780 Chain D 401–780（380 aa） Fragment：Cullin-5 residues 401-780	Mutation：L407E, L439K, V440K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L407E, L439K, V440K Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299
4JGH Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5 Deposited 2013-03-01	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 D 10–386（377 aa） Fragment：unp residues 10-386	Mutation：V341R, L345D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295.15 K；0.25 M sodium citrate and 18 % (w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 3.00 Å R-free 0.248
4JGH Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5 Deposited 2013-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 10–386（377 aa） Fragment：unp residues 10-386	Mutation：V341R, L345D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295.15 K；0.25 M sodium citrate and 18 % (w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 3.00 Å R-free 0.248
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct 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 U 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 3 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 9 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain w 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain O 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain V 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain f 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain l 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain r 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain x 12–321（310 aa） Fragment：UNP residues 12-321	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
6V9I cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) Deposited 2019-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–780（779 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20	Resolution 5.20 Å
7ONI Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2* Deposited 2021-05-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–780（780 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8EI2 Crystal structure of the N-terminal domain of CUL5 in complex with H314, a Helicon Polypeptide Deposited 2022-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–386（386 aa） Fragment：N-terminal domain	Not recorded	WHL N,N'-(1,4-phenylene)diacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v PEG 8000, 0.1M MES Sodium Salt pH6.5, 0.2M Ammonium Sulfate, 4% v/v 1,3-Propanediol	Resolution 2.80 Å R-free 0.357
8FVJ Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain 2 11–320（310 aa） Chain 7 11–320（310 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain J 1–780（780 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9OMA Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1) Deposited 2025-05-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–780（780 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
9OMF Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1) Deposited 2025-05-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–780（780 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.72 Å
9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–780（780 aa）	Not recorded	ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.97 Å
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 1–780（780 aa）	Not recorded	FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å

13 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CUL5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–780； UniProt 1–780

E3 ubiquitin-protein ligase ARIH2

Homo sapiens

UniProt O95376

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 H； UniProt 1–493	Not recorded	L3A2-1 × 1 RING-box protein 2 × 1 （Q9UBF6） Cullin-5 × 1 （Q93034） ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9SDY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7OD1 Crystal structure of RBR ubiquitin ligase ARIH2 Deposited 2021-04-28	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 1–493（493 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 8.5, 20 % PEG 3350	Resolution 2.45 Å R-free 0.262
7OD1 Crystal structure of RBR ubiquitin ligase ARIH2 Deposited 2021-04-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–493（493 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 8.5, 20 % PEG 3350	Resolution 2.45 Å R-free 0.262
7ONI Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2* Deposited 2021-05-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–493（493 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 1–493（493 aa）	Not recorded	ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.97 Å
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 1–493（493 aa）	Mutation：L381A,E382A,E455A,	FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å

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

View Construct and Data Evidence

UniProt name	ARI2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–493； UniProt 1–493

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9sdy
Deposition date deposition_date	2025-08-15
Structure title title	Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
Keywords keywords	Complex, Ligase; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	45.12 Å
Radius of gyration Rg (electron density) rg_electron	45.32 Å
Forward intensity I(0) i0	256329000.00
Molecular weight molecular_weight	129420.0 kDa
Excluded volume excluded_volume	161350 Å³
Envelope volume envelope_volume	254650 Å³
Hydration-shell volume shell_volume	49658 Å³
Envelope diameter envelope_diameter	152.7 Å
Shell Rg shell_rg	46.15 Å
Envelope Rg envelope_rg	44.54 Å
Shape Rg shape_rg	45.37 Å
Total Rg total_rg	45.21 Å
Total atoms total_atoms	9073
Residues n_residues	1172
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

▼

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

Maximum dimension Dmax dmax	147.7 Å
Rg (real space) rg_real	45.16 Å
Rg uncertainty (real space) rg_real_error	1.30 Å
I(0) (real space) i0_real	2.5630e+08
I(0) uncertainty (real space) i0_real_error	4.4250e+06
Rg (reciprocal space) rg_reciprocal	45.12 Å
I(0) (reciprocal space) i0_reciprocal	256300000.0000
Solution quality estimate total_estimate	0.8960
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.6 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.708
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14160000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.855

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	L3A2-1
Molecular weight formula_weight	17854.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	9073

MVAASSRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RING-box protein 2
Molecular weight formula_weight	12697.4 kDa
EC 编号 ec_number	2.3.2.27,2.3.2.32
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MADVEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

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	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Cullin-5
Molecular weight formula_weight	91085.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQDDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTPLSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA

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	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	E3 ubiquitin-protein ligase ARIH2
Molecular weight formula_weight	57893.8 kDa
EC 编号 ec_number	2.3.2.31
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAEQRRRTLLKDFHDT

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.060 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.06 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	191502

fit	/app/data/saxs_computation/sd/9sdy/9sdy.fit
pddf	/app/data/pr_computation/sd/9sdy/9sdy.pr.out
profile	/app/data/saxs_computation/sd/9sdy/9sdy.dat

Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2

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

RING-box protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Cullin-5

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase ARIH2

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

冷冻电镜 EM 3D

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)