Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.79 kDa 
• Atom Count: 2901 
• Modelled Residue Count: 314 
• Deposited Residue Count: 331 
• Unique protein chains: 2

2GRO

Crystal Structure of human RanGAP1-Ubc9-N85Q

• DOI: 10.2210/pdb2GRO/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-24 Released: 2006-05-30 
• Deposition Author(s): Yunus, A.A., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.185 

Literature

Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.

Yunus, A.A., Lima, C.D.

(2006) Nat Struct Mol Biol 13: 491-499

• PubMed: 16732283 
• DOI: 10.1038/nsmb1104
• Primary Citation of Related Structures:  
  2GRR, 2GRQ, 2GRP, 2GRO, 2GRN


• PubMed Abstract: 
  

E2 conjugating proteins that transfer ubiquitin and ubiquitin-like modifiers to substrate lysine residues must first activate the lysine nucleophile for conjugation. Genetic complementation revealed three side chains of the E2 Ubc9 that were crucial for normal growth. Kinetic analysis revealed modest binding defects but substantially lowered catalytic rates for these mutant alleles with respect to wild-type Ubc9. X-ray structures for wild-type and mutant human Ubc9-RanGAP1 complexes showed partial loss of contacts to the substrate lysine in mutant complexes. Computational analysis predicted pK perturbations for the substrate lysine, and Ubc9 mutations weakened pK suppression through improper side chain coordination. Biochemical studies with p53, RanGAP1 and the Nup358/RanBP2 E3 were used to determine rate constants and pK values, confirming both structural and computational predictions. It seems that Ubc9 uses an indirect mechanism to activate lysine for conjugation that may be conserved among E2 family members.

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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	161	Homo sapiens	Mutation(s): 1  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
Ran GTPase-activating protein 1	B	170	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.185 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.295	α = 72.58
b = 44.785	β = 72.06
c = 61.027	γ = 75.45

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-24 
• Released Date: 2006-05-30 
Deposition Author(s): Yunus, A.A., Lima, C.D.

Revision History  

• Version 1.0: 2006-05-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description