4LAD

Crystal Structure of the Ube2g2:RING-G2BR complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.

Das, R., Liang, Y.H., Mariano, J., Li, J., Huang, T., King, A., Tarasov, S.G., Weissman, A.M., Ji, X., Byrd, R.A.

(2013) EMBO J 32: 2504-2516

  • DOI: 10.1038/emboj.2013.174
  • Primary Citation of Related Structures:  
    2LXH, 2LXP, 4LAD

  • PubMed Abstract: 

    • RING finger proteins constitute the large majority of ubiquitin ligases (E3s) and function by interacting with ubiquitin-conjugating enzymes (E2s) charged with ubiquitin. How low-affinity RING-E2 interactions result in highly processive substrate ubiquitination is largely unknown ...

    RING finger proteins constitute the large majority of ubiquitin ligases (E3s) and function by interacting with ubiquitin-conjugating enzymes (E2s) charged with ubiquitin. How low-affinity RING-E2 interactions result in highly processive substrate ubiquitination is largely unknown. The RING E3, gp78, represents an excellent model to study this process. gp78 includes a high-affinity secondary binding region for its cognate E2, Ube2g2, the G2BR. The G2BR allosterically enhances RING:Ube2g2 binding and ubiquitination. Structural analysis of the RING:Ube2g2:G2BR complex reveals that a G2BR-induced conformational effect at the RING:Ube2g2 interface is necessary for enhanced binding of RING to Ube2g2 or Ube2g2 conjugated to Ub. This conformational effect and a key ternary interaction with conjugated ubiquitin are required for ubiquitin transfer. Moreover, RING:Ube2g2 binding induces a second allosteric effect, disrupting Ube2g2:G2BR contacts, decreasing affinity and facilitating E2 exchange. Thus, gp78 is a ubiquitination machine where multiple E2-binding sites coordinately facilitate processive ubiquitination.

    Organizational Affiliation: 

    Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 G2A165Homo sapiensMutation(s): 0 
Gene Names: UBE2G2, Ubiquitin-conjugating enzyme E2G2 isoform 1, UBC7
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60604
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase AMFRB150Homo sapiensMutation(s): 0 
Gene Names: AMFR, Autocrine motility factor receptor, RNF45
EC: 6.3.2 (PDB Primary Data), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV5 (Homo sapiens)
Explore Q9UKV5 
Go to UniProtKB:  Q9UKV5
PHAROS:  Q9UKV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKV5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXL
Query on OXL
Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]		OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.246α = 90
b = 58.246β = 90
c = 158.431γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description