6BM8

Crystal structure of glycoprotein B from Herpes Simplex Virus type I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/s41594-018-0060-6
  • Primary Citation of Related Structures:  

  • 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 repor ...

    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.


    Organizational Affiliation

    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA. katya.heldwein@tufts.edu.,National Biomedical Center for Advanced Electron Spin Resonance Technology (ACERT), Cornell University, Ithaca, NY, USA.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein B
A
833Human herpesvirus 1 (strain 17)Mutation(s): 0 
Gene Names: gB
Find proteins for P10211 (Human herpesvirus 1 (strain 17))
Go to UniProtKB:  P10211
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.269 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 118.597α = 90.00
b = 118.597β = 90.00
c = 800.576γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1R21AI107171
National Institutes of Health/National Institute of General Medical SciencesUnited States1F32GM115060
Burroughs Welcome FundUnited StatesInvestigators in the Pathogenesis of Infectious Diseases

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection