6VLK

A varicella-zoster virus glycoprotein

• PDB DOI:  https://doi.org/10.2210/pdb6VLK/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human herpesvirus 3 strain Oka vaccine
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2020-01-24 Released: 2020-07-15 
• Deposition Author(s): Xing, Y.
• 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: 2.45 Å
• R-Value Free: 0.228 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

A glycoprotein B-neutralizing antibody structure at 2.8 angstrom uncovers a critical domain for herpesvirus fusion initiation.

Oliver, S.L., Xing, Y., Chen, D.H., Roh, S.H., Pintilie, G.D., Bushnell, D.A., Sommer, M.H., Yang, E., Carfi, A., Chiu, W., Arvin, A.M.

(2020) Nat Commun 11: 4141-4141

• PubMed: 32811830 
• DOI: https://doi.org/10.1038/s41467-020-17911-0
• Primary Citation of Related Structures:  
  6VLK, 6VN1


• PubMed Abstract: 
  

Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies.

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Organizational Affiliation: 

Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 173.08 kDa 
• Atom Count: 9,766 
• Modelled Residue Count: 1,167 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B	A, B	744	Human herpesvirus 3 strain Oka vaccine	Mutation(s): 5  Gene Names: gB, ORF31
UniProt
Find proteins for Q4JR05 (Varicella-zoster virus (strain Oka vaccine)) Explore Q4JR05  Go to UniProtKB:  Q4JR05

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.228 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.318	α = 90
b = 118.318	β = 90
c = 749.026	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Xing, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AI102546, P41GM103832, R01GM079429 and S10OD021600

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2020-09-02
  Changes: Database references, Structure summary