5YS6 | pdb_00005ys6

Structure of the ectodomain of pseudorabies virus glycoproten B

• PDB DOI: https://doi.org/10.2210/pdb5YS6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Suid alphaherpesvirus 1
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2017-12-27 
• Deposition Author(s): Hu, X.L., Yang, F.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Two classes of protective antibodies against pseudorabies virus variant glycoprotein B: implications for vaccine design

Li, X.D., Yang, F.L., Hu, X.L.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.46 kDa 
• Atom Count: 4,582 
• Modeled Residue Count: 572 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRV glycoproten B	A	702	Suid alphaherpesvirus 1	Mutation(s): 0  Gene Names: gB
UniProt
Find proteins for T2FL65 (Suid herpesvirus 1) Explore T2FL65  Go to UniProtKB:  T2FL65

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.288	α = 90
b = 100.288	β = 90
c = 272.918	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Hu, X.L., Yang, F.L.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary