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)

Biological Assembly Evidence: gel filtration, homology

Macromolecule Content

• Total Structure Weight: 94.98 kDa 
• Atom Count: 5391 
• Residue Count: 665 
• Unique protein chains: 1

6BM8

Crystal structure of glycoprotein B from Herpes Simplex Virus type I

• DOI: 10.2210/pdb6BM8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human alphaherpesvirus 1
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2018-05-16 
• Deposition Author(s): Cooper, R.S., Heldwein, E.E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Burroughs Welcome Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 

Literature

Structural basis for membrane anchoring and fusion regulation of the herpes simplex virus fusogen gB.

Cooper, R.S., Georgieva, E.R., Borbat, P.P., Freed, J.H., Heldwein, E.E.

(2018) Nat Struct Mol Biol 25: 416-424

• PubMed: 29728654 
• DOI: 10.1038/s41594-018-0060-6
• Primary Citation of Related Structures:  
  5V2S, 6BM8


• PubMed Abstract: 
  

Viral fusogens merge viral and cell membranes during cell penetration. Their ectodomains drive fusion by undergoing large-scale refolding, but little is known about the functionally important regions located within or near the membrane. Here we report the crystal structure of full-length glycoprotein B (gB), the fusogen from herpes simplex virus, complemented by electron spin resonance measurements. The membrane-proximal (MPR), transmembrane (TMD), and cytoplasmic (CTD) domains form a uniquely folded trimeric pedestal beneath the ectodomain, which balances dynamic flexibility with extensive, stabilizing membrane interactions. The postfusion conformation of the ectodomain suggests that the CTD likewise adopted the postfusion form. However, hyperfusogenic mutations, which destabilize the prefusion state of gB, target key interfaces and structural motifs that reinforce the observed CTD structure. Thus, a similar CTD structure must stabilize gB in its prefusion state. Our data suggest a model for how this dynamic, membrane-dependent 'clamp' controls the fusogenic refolding of gB.

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Organizational Affiliation: 

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B	A	833	Human alphaherpesvirus 1	Mutation(s): 0  Gene Names: UL27, gB, HHV1gp041
Find proteins for P10211 (Human herpesvirus 1 (strain 17)) Explore P10211  Go to UniProtKB:  P10211

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.597	α = 90
b = 118.597	β = 90
c = 800.576	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-13 
• Released Date: 2018-05-16 
Deposition Author(s): Cooper, R.S., Heldwein, E.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R21AI107171
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1F32GM115060
Burroughs Welcome Fund	United States	Investigators in the Pathogenesis of Infectious Diseases

Revision History 

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary