Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 163.30 kDa 
• Atom Count: 10922 
• Residue Count: 1441 
• Unique protein chains: 1

2B9B

Structure of the Parainfluenza Virus 5 F Protein in its Metastable, Pre-fusion Conformation

• DOI: 10.2210/pdb2B9B/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Mammalian rubulavirus 5
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2005-10-11 Released: 2006-01-24 
• Deposition Author(s): Yin, H.-S., Wen, X., Paterson, R.G., Lamb, R.A., Jardetzky, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.259 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Structure of the parainfluenza virus 5 F protein in its metastable, prefusion conformation

Yin, H.-S., Wen, X., Paterson, R.G., Lamb, R.A., Jardetzky, T.S.

(2006) Nature 439: 38-44

• PubMed: 16397490 
• DOI: 10.1038/nature04322
• Primary Citation of Related Structures:  
  2B9B


• PubMed Abstract: 
  

Enveloped viruses have evolved complex glycoprotein machinery that drives the fusion of viral and cellular membranes, permitting entry of the viral genome into the cell. For the paramyxoviruses, the fusion (F) protein catalyses this membrane merger and entry step, and it has been postulated that the F protein undergoes complex refolding during this process. Here we report the crystal structure of the parainfluenza virus 5 F protein in its prefusion conformation, stabilized by the addition of a carboxy-terminal trimerization domain. The structure of the F protein shows that there are profound conformational differences between the pre- and postfusion states, involving transformations in secondary and tertiary structure. The positions and structural transitions of key parts of the fusion machinery, including the hydrophobic fusion peptide and two helical heptad repeat regions, clarify the mechanism of membrane fusion mediated by the F protein.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois 60208-3500, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C	497	Mammalian rubulavirus 5	Mutation(s): 0  Gene Names: F
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	A, B, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.259 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.206	α = 90
b = 259.864	β = 90
c = 154.012	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
CNS	refinement
SHARP	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
DM	phasing
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-11 
• Released Date: 2006-01-24 
Deposition Author(s): Yin, H.-S., Wen, X., Paterson, R.G., Lamb, R.A., Jardetzky, T.S.

Revision History 

• Version 1.0: 2006-01-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary