Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.74 kDa 
• Atom Count: 3592 
• Residue Count: 455 
• Unique protein chains: 4

1Z5S

Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2

• DOI: 10.2210/pdb1Z5S/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-19 Released: 2005-06-07 
• Deposition Author(s): Reverter, D., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.290 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Literature

Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.

Reverter, D., Lima, C.D.

(2005) Nature 435: 687-692

• PubMed: 15931224 
• DOI: 10.1038/nature03588
• Primary Citation of Related Structures:  
  1Z5S


• PubMed Abstract: 
  

SUMO-1 (for small ubiquitin-related modifier) belongs to the ubiquitin (Ub) and ubiquitin-like (Ubl) protein family. SUMO conjugation occurs on specific lysine residues within protein targets, regulating pathways involved in differentiation, apoptosis, the cell cycle and responses to stress by altering protein function through changes in activity or cellular localization or by protecting substrates from ubiquitination. Ub/Ubl conjugation occurs in sequential steps and requires the concerted action of E2 conjugating proteins and E3 ligases. In addition to being a SUMO E3, the nucleoporin Nup358/RanBP2 localizes SUMO-conjugated RanGAP1 to the cytoplasmic face of the nuclear pore complex by means of interactions in a complex that also includes Ubc9, the SUMO E2 conjugating protein. Here we describe the 3.0-A crystal structure of a four-protein complex of Ubc9, a Nup358/RanBP2 E3 ligase domain (IR1-M) and SUMO-1 conjugated to the carboxy-terminal domain of RanGAP1. Structural insights, combined with biochemical and kinetic data obtained with additional substrates, support a model in which Nup358/RanBP2 acts as an E3 by binding both SUMO and Ubc9 to position the SUMO-E2-thioester in an optimal orientation to enhance conjugation.

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Organizational Affiliation: 

Structural Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 I	A	158	Homo sapiens	Mutation(s): 0  Gene Names: UBE2I, UBC9, UBCE9 EC: 6.3.2.19 (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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3C	B	82	Homo sapiens	Mutation(s): 0  Gene Names: UBL1, SMT3C, SMT3H3, SUMO1, OK/SW-cl.43
Find proteins for P63165 (Homo sapiens) Explore P63165  Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165 GTEx  ENSG00000116030

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran GTPase-activating protein 1	C	172	Homo sapiens	Mutation(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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran-binding protein 2	D	83	Homo sapiens	Mutation(s): 0  Gene Names: RANBP2, NUP358 EC: 2.3.2
Find proteins for P49792 (Homo sapiens) Explore P49792  Go to UniProtKB:  P49792
NIH Common Fund Data Resources
PHAROS  P49792 GTEx  ENSG00000153201

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.290 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.123	α = 90
b = 157.123	β = 90
c = 59.613	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-19 
• Released Date: 2005-06-07 
Deposition Author(s): Reverter, D., Lima, C.D.

Revision History 

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance