Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 81.86 kDa 
• Atom Count: 5355 
• Residue Count: 655 
• Unique protein chains: 3

3W9E

Structure of Human Monoclonal Antibody E317 Fab Complex with HSV-2 gD

• DOI: 10.2210/pdb3W9E/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human herpesvirus 2 strain HG52, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-04-03 Released: 2013-10-02 
• Deposition Author(s): Lee, C.C., Lin, L.L., Wang, A.H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

Structural basis for the antibody neutralization of herpes simplex virus

Lee, C.C., Lin, L.L., Chan, W.E., Ko, T.P., Lai, J.S., Wang, A.H.J.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1935-1945

• PubMed: 24100313 
• DOI: 10.1107/S0907444913016776
• Primary Citation of Related Structures:  
  3W9E, 3W9D


• PubMed Abstract: 
  

Glycoprotein D (gD) of herpes simplex virus (HSV) binds to a host cell surface receptor, which is required to trigger membrane fusion for virion entry into the host cell. gD has become a validated anti-HSV target for therapeutic antibody development. The highly inhibitory human monoclonal antibody E317 (mAb E317) was previously raised against HSV gD for viral neutralization. To understand the structural basis of antibody neutralization, crystals of the gD ectodomain bound to the E317 Fab domain were obtained. The structure of the complex reveals that E317 interacts with gD mainly through the heavy chain, which covers a large area for epitope recognition on gD, with a flexible N-terminal and C-terminal conformation. The epitope core structure maps to the external surface of gD, corresponding to the binding sites of two receptors, herpesvirus entry mediator (HVEM) and nectin-1, which mediate HSV infection. E317 directly recognizes the gD-nectin-1 interface and occludes the HVEM contact site of gD to block its binding to either receptor. The binding of E317 to gD also prohibits the formation of the N-terminal hairpin of gD for HVEM recognition. The major E317-binding site on gD overlaps with either the nectin-1-binding residues or the neutralizing antigenic sites identified thus far (Tyr38, Asp215, Arg222 and Phe223). The epitopes of gD for E317 binding are highly conserved between two types of human herpesvirus (HSV-1 and HSV-2). This study enables the virus-neutralizing epitopes to be correlated with the receptor-binding regions. The results further strengthen the previously demonstrated therapeutic and diagnostic potential of the E317 antibody.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein D	C	306	Human herpesvirus 2 strain HG52	Mutation(s): 0  Gene Names: gD, US6
Find proteins for Q69467 (Human herpesvirus 2 (strain HG52)) Explore Q69467  Go to UniProtKB:  Q69467

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab heavy chain	A	222	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab light chain	B	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	D	4		N-Glycosylation

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.029	α = 90
b = 91.087	β = 90
c = 141.537	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-03 
• Released Date: 2013-10-02 
Deposition Author(s): Lee, C.C., Lin, L.L., Wang, A.H.J.

Revision History 

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary