3UIO

Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2.

Gareau, J.R., Reverter, D., Lima, C.D.

(2012) J Biol Chem 287: 4740-4751

  • DOI: 10.1074/jbc.M111.321141
  • Primary Citation of Related Structures:  
    3UIO, 3UIP, 3UIN

  • PubMed Abstract: 

    • The RanBP2 nucleoporin contains an internal repeat domain (IR1-M-IR2) that catalyzes E3 ligase activity and forms a stable complex with SUMO-modified RanGAP1 and UBC9 at the nuclear pore complex. RanBP2 exhibits specificity for SUMO1 as RanGAP1-SUMO1 ...

    The RanBP2 nucleoporin contains an internal repeat domain (IR1-M-IR2) that catalyzes E3 ligase activity and forms a stable complex with SUMO-modified RanGAP1 and UBC9 at the nuclear pore complex. RanBP2 exhibits specificity for SUMO1 as RanGAP1-SUMO1/UBC9 forms a more stable complex with RanBP2 compared with RanGAP1-SUMO2 that results in greater protection of RanGAP-SUMO1 from proteases. The IR1-M-IR2 SUMO E3 ligase activity also shows a similar preference for SUMO1. We utilized deletions and domain swap constructs in protease protection assays and automodification assays to define RanBP2 domains responsible for RanGAP1-SUMO1 protection and SUMO1-specific E3 ligase activity. Our data suggest that elements in both IR1 and IR2 exhibit specificity for SUMO1. IR1 protects RanGAP1-SUMO1/UBC9 and functions as the primary E3 ligase of RanBP2, whereas IR2 retains the ability to interact with SUMO1 to promote SUMO1-specific E3 ligase activity. To determine the structural basis for SUMO1 specificity, a hybrid IR1 construct and IR1 were used to determine three new structures for complexes containing UBC9 with RanGAP1-SUMO1/2. These structures show more extensive contacts among SUMO, UBC9, and RanBP2 in complexes containing SUMO1 compared with SUMO2 and suggest that differences in SUMO specificity may be achieved through these subtle conformational differences.

    Organizational Affiliation: 

    Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9A158Homo sapiensMutation(s): 0 
Gene Names: UBC9, UBCE9, UBE2I
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 2B80Homo sapiensMutation(s): 0 
Gene Names: SMT3A, SMT3H2, SUMO2, SMT3B
Find proteins for P61956 (Homo sapiens)
Explore P61956 
Go to UniProtKB:  P61956
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PHAROS  P61956
GTEx  ENSG00000188612
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1C171Homo sapiensMutation(s): 0 
Gene Names: KIAA1835, RANGAP1, SD
Find proteins for P46060 (Homo sapiens)
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Go to UniProtKB:  P46060
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PHAROS  P46060
GTEx  ENSG00000100401
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
E3 SUMO-protein ligase RanBP2D67Homo sapiensMutation(s): 5 
Gene Names: NUP358, RANBP2
EC: 2.3.2
Find proteins for P49792 (Homo sapiens)
Explore P49792 
Go to UniProtKB:  P49792
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PHAROS  P49792
GTEx  ENSG00000153201
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD		AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.351α = 90
b = 151.351β = 90
c = 57.442γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-04
    Changes: Database references
  • Version 1.2: 2013-06-26
    Changes: Database references