2O25

Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9

• PDB DOI: https://doi.org/10.2210/pdb2O25/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-29 Released: 2007-01-16 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Starting Models: experimental

Literature

A Novel and Unexpected Complex Between the SUMO-1-Conjugating Enzyme UBC9 and the Ubiquitin-Conjugating Enzyme E2-25 kDa

Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.5 kDa 
• Atom Count: 5,687 
• Modelled Residue Count: 709 
• Deposited Residue Count: 724 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2-25 kDa	A, B	202	Homo sapiens	Mutation(s): 0  Gene Names: HIP2, LIG EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61086 (Homo sapiens) Explore P61086  Go to UniProtKB:  P61086
PHAROS:  P61086 GTEx:  ENSG00000078140

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-1-conjugating enzyme UBC9	C, D	160	Homo sapiens	Mutation(s): 0  Gene Names: UBE2I, UBC9, UBCE9 EC: 6.3.2.19 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens) Explore P63279  Go to UniProtKB:  P63279
PHAROS:  P63279 GTEx:  ENSG00000103275

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.874	α = 85.05
b = 68.498	β = 80.85
c = 91.277	γ = 75.83

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description