1KPS

Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1.

Bernier-Villamor, V.Sampson, D.A.Matunis, M.J.Lima, C.D.

(2002) Cell 108: 345-356


  • PubMed Abstract: 
  • E2 enzymes catalyze attachment of ubiquitin and ubiquitin-like proteins to lysine residues directly or through E3-mediated reactions. The small ubiquitin-like modifier SUMO regulates nuclear transport, stress response, and signal transduction in euka ...

    E2 enzymes catalyze attachment of ubiquitin and ubiquitin-like proteins to lysine residues directly or through E3-mediated reactions. The small ubiquitin-like modifier SUMO regulates nuclear transport, stress response, and signal transduction in eukaryotes and is essential for cell-cycle progression in yeast. In contrast to most ubiquitin conjugation, the SUMO E2 enzyme Ubc9 is sufficient for substrate recognition and lysine modification of known SUMO targets. Crystallographic analysis of a complex between mammalian Ubc9 and a C-terminal domain of RanGAP1 at 2.5 A reveals structural determinants for recognition of consensus SUMO modification sequences found within SUMO-conjugated proteins. Structure-based mutagenesis and biochemical analysis of Ubc9 and RanGAP1 reveal distinct motifs required for substrate binding and SUMO modification of p53, IkappaBalpha, and RanGAP1.


    Organizational Affiliation

    Biochemistry Department, Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein SUMO-1 conjugating enzyme
A, C
159Homo sapiensGene Names: UBE2I (UBC9, UBCE9)
EC: 6.3.2.-
Find proteins for P63279 (Homo sapiens)
Go to Gene View: UBE2I
Go to UniProtKB:  P63279
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ran-GTPase activating protein 1
B, D
171Mus musculusGene Names: Rangap1 (Fug1)
Find proteins for P46061 (Mus musculus)
Go to UniProtKB:  P46061
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.531α = 90.00
b = 126.509β = 90.00
c = 72.639γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
RESOLVEphasing
RESOLVEmodel building
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection