9SDY | pdb_00009sdy

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

• PDB DOI: https://doi.org/10.2210/pdb9SDY/pdb
• EM Map EMD-54794: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-08-15 Released: 2025-12-24 
• Deposition Author(s): Schulman, B.A., Du, J.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

E2 Variants for Probing E3 Ubiquitin Ligase Activities

Du, J., Schulman, B.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 179.99 kDa 
• Atom Count: 9,073 
• Modeled Residue Count: 1,172 
• Deposited Residue Count: 1,541 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L3A2-1	A [auth G]	155	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING-box protein 2	B [auth R]	113	Homo sapiens	Mutation(s): 0  Gene Names: RNF7, RBX2, ROC2, SAG EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF6 (Homo sapiens) Explore Q9UBF6  Go to UniProtKB:  Q9UBF6
PHAROS:  Q9UBF6 GTEx:  ENSG00000114125

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-5	C	780	Homo sapiens	Mutation(s): 0  Gene Names: CUL5, VACM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q93034 (Homo sapiens) Explore Q93034  Go to UniProtKB:  Q93034
PHAROS:  Q93034 GTEx:  ENSG00000166266

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase ARIH2	D [auth H]	493	Homo sapiens	Mutation(s): 0  Gene Names: ARIH2, ARI2, TRIAD1, HT005 EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O95376 (Homo sapiens) Explore O95376  Go to UniProtKB:  O95376
PHAROS:  O95376 GTEx:  ENSG00000177479

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth R], F [auth R], G [auth R], H, I [auth H], J [auth H], K [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Schulman, B.A., Du, J.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SCHU3196/1-1

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release