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 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

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9AD161Homo sapiensMutation(s): 1 
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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 2BE83Homo sapiensMutation(s): 0 
Gene Names: SUMO2SMT3BSMT3H2
Find proteins for P61956 (Homo sapiens)
Explore P61956 
Go to UniProtKB:  P61956
NIH Common Fund Data Resources
PHAROS  P61956
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1CF171Homo sapiensMutation(s): 0 
Gene Names: RANGAP1KIAA1835SD
Find proteins for P46060 (Homo sapiens)
Explore P46060 
Go to UniProtKB:  P46060
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PHAROS  P46060
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein 451G65Homo sapiensMutation(s): 0 
Gene Names: ZNF451COASTERKIAA0576KIAA1702
EC: 2.3.2
Find proteins for Q9Y4E5 (Homo sapiens)
Explore Q9Y4E5 
Go to UniProtKB:  Q9Y4E5
NIH Common Fund Data Resources
PHAROS  Q9Y4E5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, C, F
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
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



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 

  • 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