2GUM

Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I

PDB DOI: https://doi.org/10.2210/pdb2GUM/pdb

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

Deposited: 2006-05-01 Released: 2006-07-25
Deposition Author(s): Heldwein, E.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.275
R-Value Work: 0.248
R-Value Observed: 0.248

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of glycoprotein B from herpes simplex virus 1.

Heldwein, E.E., Lou, H., Bender, F.C., Cohen, G.H., Eisenberg, R.J., Harrison, S.C.

(2006) Science 313: 217-220

PubMed: 16840698 Search on PubMed
DOI: https://doi.org/10.1126/science.1126548
Primary Citation of Related Structures:
2GUM

PubMed Abstract:
Glycoprotein B (gB) is the most conserved component of the complex cell-entry machinery of herpes viruses. A crystal structure of the gB ectodomain from herpes simplex virus type 1 reveals a multidomain trimer with unexpected homology to glycoprotein G from vesicular stomatitis virus (VSV G). An alpha-helical coiled-coil core relates gB to class I viral membrane fusion glycoproteins; two extended beta hairpins with hydrophobic tips, homologous to fusion peptides in VSV G, relate gB to class II fusion proteins. Members of both classes accomplish fusion through a large-scale conformational change, triggered by a signal from a receptor-binding component. The domain connectivity within a gB monomer would permit such a rearrangement, including long-range translocations linked to viral and cellular membranes.

Organizational Affiliation

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA. heldwein@crystal.harvard.edu

Macromolecule Content

Total Structure Weight: 215.1 kDa
Atom Count: 14,223
Modelled Residue Count: 1,732
Deposited Residue Count: 1,884
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein B	A, B, C	628	Human alphaherpesvirus 1 strain KOS	Mutation(s): 0 Gene Names: GB, UL27
UniProt
Find proteins for P06437 (Human herpesvirus 1 (strain KOS)) Explore P06437 Go to UniProtKB: P06437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C]	D [auth A], E [auth B], F [auth B], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.275
R-Value Work: 0.248
R-Value Observed: 0.248
Space Group: P 1
Diffraction Data: https://doi.org/10.15785/SBGRID/120
Diffraction Data: https://doi.org/10.15785/SBGRID/122

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.959	α = 67.04
b = 100.039	β = 77.99
c = 100.133	γ = 70.31

Software Package:

Software Name	Purpose
ADSC	data collection
DENZO	data reduction
SnB	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-07-25

Deposition Author(s):

Heldwein, E.E.

Revision History (Full details and data files)

Version 1.0: 2006-07-25
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description