5I2M | pdb_00005i2m

CRYSTAL STRUCTURE OF VSV-INDIANA (MUDD-SUMMERS STRAIN) GLYCOPROTEIN UNDER ITS ACIDIC CONFORMATION

• PDB DOI: https://doi.org/10.2210/pdb5I2M/pdb
• Entry: 5I2M supersedes: 2CMZ

• Classification: MEMBRANE PROTEIN
• Organism(s): Vesicular stomatitis Indiana virus strain Mudd-Summers
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-02-09 Released: 2016-02-24 
• Deposition Author(s): Roche, S., Bressanelli, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of the low-pH form of the vesicular stomatitis virus glycoprotein G.

Roche, S., Bressanelli, S., Rey, F.A., Gaudin, Y.

(2006) Science 313: 187-191

• PubMed: 16840692 
• DOI: https://doi.org/10.1126/science.1127683
• Primary Citation Related Structures: 
  5I2M


• PubMed Abstract: 
  

  The vesicular stomatitis virus has an atypical membrane fusion glycoprotein (G) exhibiting a pH-dependent equilibrium between two forms at the virus surface. Membrane fusion is triggered during the transition from the high- to low-pH form. The structure of G in its low-pH form shows the classic hairpin conformation observed in all other fusion proteins in their postfusion conformation, in spite of a novel fold combining features of fusion proteins from classes I and II. The structure provides a framework for understanding the reversibility of the G conformational change. Unexpectedly, G is homologous to gB of herpesviruses, which raises important questions on viral evolution.

---

Organizational Affiliation: 
• CNRS, Unité Mixte de Recherche (UMR) 2472, Institut Fédératif de Recherche (IFR) 115, Virologie Moléculaire et Structurale, 91198, Gif sur Yvette, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 143.84 kDa 
• Atom Count: 10,314 
• Modeled Residue Count: 1,227 
• Deposited Residue Count: 1,266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G	A, B, C	422	Vesicular stomatitis Indiana virus strain Mudd-Summers	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0C2X0 (Vesicular stomatitis Indiana virus (strain Mudd-Summers)) Explore P0C2X0  Go to UniProtKB:  P0C2X0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	D [auth A], E [auth B], F [auth B], G [auth B], H [auth C]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
CA	I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.27	α = 90
b = 224.2	β = 90
c = 375.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Roche, S., Bressanelli, S.
• This entry supersedes: 2CMZ

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary