5D2M

Complex between human SUMO2-RANGAP1, UBC9 and ZNF451

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.5 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
  • Primary Citation of Related Structures:  
    5D2M

  • 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 biochemical and structural data that define the N-terminal domain of the Homo sapiens ZNF451 as the catalytic module for SUMO E3 ligase activity ...

    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: 

    Howard Hughes Medical Institute, Sloan Kettering Institute, New York, New York, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9 A, D161Homo sapiensMutation(s): 1 
Gene Names: UBE2I, UBC9, UBCE9
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
GTEx:  ENSG00000103275
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 2 B, E83Homo sapiensMutation(s): 0 
Gene Names: SUMO2, SMT3B, SMT3H2
Find proteins for P61956 (Homo sapiens)
Explore P61956 
Go to UniProtKB:  P61956
NIH Common Fund Data Resources
PHAROS:  P61956
GTEx:  ENSG00000188612
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1 C, F171Homo sapiensMutation(s): 0 
Gene Names: RANGAP1, KIAA1835, SD
Find proteins for P46060 (Homo sapiens)
Explore P46060 
Go to UniProtKB:  P46060
NIH Common Fund Data Resources
PHAROS:  P46060
GTEx:  ENSG00000100401
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein 451 G65Homo sapiensMutation(s): 0 
Gene Names: ZNF451, COASTER, KIAA0576, KIAA1702
EC: 2.3.2
Find proteins for Q9Y4E5 (Homo sapiens)
Explore Q9Y4E5 
Go to UniProtKB:  Q9Y4E5
NIH Common Fund Data Resources
PHAROS:  Q9Y4E5
GTEx:  ENSG00000112200
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.24α = 90
b = 115.06β = 90
c = 130.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM065872

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence