5I2S

PREFUSION FORM OF THE VESICULAR STOMATITIS VIRUS GLYCOPROTEIN G ECTODOMAIN

• PDB DOI: https://doi.org/10.2210/pdb5I2S/pdb
• Entry: 5I2S supersedes: 2J6J, 2J6J

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


• Deposited: 2016-02-09 Released: 2016-03-02 
• Deposition Author(s): Roche, S., Bressanelli, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.33 kDa 
• Atom Count: 3,308 
• Modelled Residue Count: 413 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G	A	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
YB	D [auth A], E [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.51	α = 90
b = 120.51	β = 90
c = 183.13	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Roche, S., Bressanelli, S.
• This entry supersedes: 2J6J, 2J6J

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary