Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53604.17 
• Atom Count: 3625 
• Residue Count: 476 
• Unique protein chains: 4

3UIO

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

• DOI: 10.2210/pdb3UIO/pdb

• Classification: Ligase/Isomerase/Protein Binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 5 


• Deposited: 2011-11-05 Released: 2011-12-28 
• Deposition Author(s): Gareau, J.R., Reverter, D., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.602 Å
• R-Value Free: 0.251 
• R-Value Work: 0.204 

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

• PubMed: 22194619 
• DOI: 10.1074/jbc.M111.321141
• Primary Citation of Related Structures:  
  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/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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SUMO-conjugating enzyme UBC9	A	158	Homo sapiens	Mutation(s): 0  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
Molecule	Chains	Sequence Length	Organism	Details
Small ubiquitin-related modifier 2	B	80	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Ran GTPase-activating protein 1	C	171	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
E3 SUMO-protein ligase RanBP2	D	67	Homo sapiens	Mutation(s): 5  Gene Names: RANBP2 (NUP358) EC: 2.3.2.-
Find proteins for P49792 (Homo sapiens) Go to Gene View: RANBP2 Go to UniProtKB:  P49792

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, D	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.602 Å
• R-Value Free: 0.251 
• R-Value Work: 0.204 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 151.351	α = 90.00
b = 151.351	β = 90.00
c = 57.442	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	refinement
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-05 
• Released Date: 2011-12-28 
• Deposition Author(s): Gareau, J.R., Reverter, D., Lima, C.D.

Revision History 

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