4GIP

Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 (PIV5) fusion protein

• PDB DOI: https://doi.org/10.2210/pdb4GIP/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Simian virus 5 (strain W3)
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-08-08 Released: 2012-09-19 
• Deposition Author(s): Welch, B.D., Liu, Y., Kors, C.A., Leser, G.P., Jardetzky, T.S., Lamb, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 161.13 kDa 
• Atom Count: 11,335 
• Modelled Residue Count: 1,368 
• Deposited Residue Count: 1,470 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F2	A, C [auth B], E [auth C]	81	Simian virus 5 (strain W3)	Mutation(s): 0  Gene Names: F
UniProt
Find proteins for P04849 (Parainfluenza virus 5 (strain W3)) Explore P04849  Go to UniProtKB:  P04849

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F1	B [auth D], D [auth E], F	409	Simian virus 5 (strain W3)	Mutation(s): 0  Gene Names: F
UniProt
Find proteins for P04849 (Parainfluenza virus 5 (strain W3)) Explore P04849  Go to UniProtKB:  P04849

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth D], I [auth D], J [auth B], K [auth E], L [auth E], M [auth E], N [auth C], O [auth C], P [auth F], Q [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.93	α = 90
b = 140.52	β = 99.84
c = 84.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Welch, B.D., Liu, Y., Kors, C.A., Leser, G.P., Jardetzky, T.S., Lamb, R.A.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary