5EJB

Crystal structure of prefusion Hendra virus F protein

• PDB DOI: https://doi.org/10.2210/pdb5EJB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Henipavirus hendraense
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-11-01 Released: 2016-01-06 
• Deposition Author(s): Wong, J.W., Jardetzky, T.S., Paterson, R.G., Lamb, R.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.283 
• R-Value Work: 0.253 
• R-Value Observed: 0.254 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 335.51 kDa 
• Atom Count: 20,415 
• Modelled Residue Count: 2,673 
• Deposited Residue Count: 3,006 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A [auth B], B [auth C], C [auth D], D [auth F], E, F [auth A]	501	Henipavirus hendraense	Mutation(s): 0  Gene Names: F
UniProt
Find proteins for O89342 (Hendra virus (isolate Horse/Autralia/Hendra/1994)) Explore O89342  Go to UniProtKB:  O89342

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	G, H, I	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	K [auth C], M [auth D], N [auth D], O [auth D], Q [auth F], R [auth F], T [auth E], U [auth E], V [auth E], W [auth E], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	AA [auth A], J [auth B], L [auth C], P [auth D], S [auth F], X [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.283 
• R-Value Work: 0.253 
• R-Value Observed: 0.254 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.61	α = 90
b = 163.5	β = 94.13
c = 147.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-06 
Deposition Author(s): Wong, J.W., Jardetzky, T.S., Paterson, R.G., Lamb, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-61050

Revision History  

• Version 1.0: 2016-01-06
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references, Derived calculations
• Version 1.2: 2016-02-10
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary