5D2M

Complex between human SUMO2-RANGAP1, UBC9 and ZNF451


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase.

Cappadocia, L.Pichler, A.Lima, C.D.

(2015) Nat.Struct.Mol.Biol. 22: 968-975

  • DOI: 10.1038/nsmb.3116

  • PubMed Abstract: 
  • E3 protein ligases enhance transfer of ubiquitin-like (Ubl) proteins from E2 conjugating enzymes to substrates by stabilizing the thioester-charged E2~Ubl in a closed configuration optimally aligned for nucleophilic attack. Here, we report biochemica ...

    E3 protein ligases enhance transfer of ubiquitin-like (Ubl) proteins from E2 conjugating enzymes to substrates by stabilizing the thioester-charged E2~Ubl in a closed configuration optimally aligned for nucleophilic attack. Here, we report biochemical and structural data that define the N-terminal domain of the Homo sapiens ZNF451 as the catalytic module for SUMO E3 ligase activity. The ZNF451 catalytic module contains tandem SUMO-interaction motifs (SIMs) bridged by a Pro-Leu-Arg-Pro (PLRP) motif. The first SIM and PLRP motif engage thioester-charged E2~SUMO while the next SIM binds a second molecule of SUMO bound to the back side of E2. We show that ZNF451 is SUMO2 specific and that SUMO modification of ZNF451 may contribute to activity by providing a second molecule of SUMO that interacts with E2. Our results are consistent with ZNF451 functioning as a bona fide SUMO E3 ligase.


    Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUMO-conjugating enzyme UBC9
A, D
161Homo sapiensMutation(s): 1 
Gene Names: UBE2I (UBC9, UBCE9)
EC: 2.3.2.-
Find proteins for P63279 (Homo sapiens)
Go to Gene View: UBE2I
Go to UniProtKB:  P63279
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 2
B, E
83Homo sapiensMutation(s): 0 
Gene Names: SUMO2 (SMT3B, SMT3H2)
Find proteins for P61956 (Homo sapiens)
Go to Gene View: SUMO2
Go to UniProtKB:  P61956
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ran GTPase-activating protein 1
C, F
171Homo sapiensMutation(s): 0 
Gene Names: RANGAP1 (KIAA1835, SD)
Find proteins for P46060 (Homo sapiens)
Go to Gene View: RANGAP1
Go to UniProtKB:  P46060
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Zinc finger protein 451
G
65Homo sapiensMutation(s): 0 
Gene Names: ZNF451 (COASTER, KIAA0576, KIAA1702)
EC: 2.3.2.-
Find proteins for Q9Y4E5 (Homo sapiens)
Go to Gene View: ZNF451
Go to UniProtKB:  Q9Y4E5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.240α = 90.00
b = 115.060β = 90.00
c = 130.980γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM065872

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2015-12-16
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence