4Y1L

Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

RWD Domain as an E2 (Ubc9)-Interaction Module.

Alontaga, A.Y.Ambaye, N.D.Li, Y.J.Vega, R.Chen, C.H.Bzymek, K.P.Williams, J.C.Hu, W.Chen, Y.

(2015) J Biol Chem 290: 16550-16559

  • DOI: 10.1074/jbc.M115.644047
  • Primary Citation of Related Structures:  
    4Y1L

  • PubMed Abstract: 
  • An RWD domain is a well conserved domain found through bioinformatic analysis of the human proteome sequence; however, its function has been unknown. Ubiquitin-like modifications require the catalysis of three enzymes generally known as E1, E2, and E ...

    An RWD domain is a well conserved domain found through bioinformatic analysis of the human proteome sequence; however, its function has been unknown. Ubiquitin-like modifications require the catalysis of three enzymes generally known as E1, E2, and E3. We solved the crystal structure of the E2 for the small ubiquitin-like modifiers (SUMO) in complex with an RWD domain and confirmed the structure using solution NMR analysis. The binding surface of RWD on Ubc9 is located near the N terminus of Ubc9 that is known to be involved in noncovalent binding of the proteins in the conjugation machinery, including a domain of E1, SUMO, and an E3 ligase. NMR data indicate that the RWD domain does not bind to SUMO and E1. The interaction between RWD and Ubc9 has a Kd of 32 ± 4 μM. Consistent with the structure and binding affinity and in contrast to a previous report, the RWD domain and RWDD3 have minimal effects on global SUMOylation. The structural and biochemical information presented here forms the basis for further investigation of the functions of RWD-containing proteins.


    Organizational Affiliation

    From the Department of Molecular Medicine and ychen@coh.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9AB158Homo sapiensMutation(s): 0 
Gene Names: UBE2IUBC9UBCE9
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P63279 (Homo sapiens)
Explore P63279 
Go to UniProtKB:  P63279
NIH Common Fund Data Resources
PHAROS  P63279
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RWD domain-containing protein 3C113Homo sapiensMutation(s): 0 
Gene Names: RWDD3RSUME
Find proteins for Q9Y3V2 (Homo sapiens)
Explore Q9Y3V2 
Go to UniProtKB:  Q9Y3V2
NIH Common Fund Data Resources
PHAROS  Q9Y3V2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.23α = 90
b = 34.86β = 98.53
c = 114.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102538
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM086171

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence