2CYX

Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)

• PDB DOI: https://doi.org/10.2210/pdb2CYX/pdb

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


• Deposited: 2005-07-08 Released: 2006-04-25 
• Deposition Author(s): Yoshikawa, S., Arai, R., Murayama, K., Imai, Y., Takahashi, R., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 

Starting Model: experimental

Literature

Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)

Arai, R., Yoshikawa, S., Murayama, K., Imai, Y., Takahashi, R., Shirouzu, M., Yokoyama, S.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 330-334

• PubMed: 16582478 
• DOI: https://doi.org/10.1107/S1744309106009006
• Primary Citation of Related Structures:  
  2CYX


• PubMed Abstract: 
  

  The human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7) is involved in protein degradation, including a process known as endoplasmic reticulum-associated degradation (ERAD). The crystal structure of human UBE2G2/UBC7 was solved at 2.56 angstroms resolution. The UBE2G2 structure comprises a single domain consisting of an antiparallel beta-sheet with four strands, five alpha-helices and two 3(10)-helices. Structural comparison of human UBE2G2 with yeast Ubc7 indicated that the overall structures are similar except for the long loop region and the C-terminal helix. Superimposition of UBE2G2 on UbcH7 in a c-Cbl-UbcH7-ZAP70 ternary complex suggested that the two loop regions of UBE2G2 interact with the RING domain in a similar way to UbcH7. In addition, the extra loop region of UBE2G2 may interact with the RING domain or its neighbouring region and may be involved in the binding specificity and stability.

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Organizational Affiliation: 

Protein Research Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.18 kDa 
• Atom Count: 4,019 
• Modelled Residue Count: 507 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 G2	A, B, C	170	Homo sapiens	Mutation(s): 0  Gene Names: UBE2G2 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60604 (Homo sapiens) Explore P60604  Go to UniProtKB:  P60604
PHAROS:  P60604 GTEx:  ENSG00000184787

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.522	α = 90
b = 87.61	β = 90
c = 157.41	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Yoshikawa, S., Arai, R., Murayama, K., Imai, Y., Takahashi, R., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description