6TM8 | pdb_00006tm8

Crystal structure of glycoprotein D of Equine Herpesvirus Type 4

• PDB DOI: https://doi.org/10.2210/pdb6TM8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Equid alphaherpesvirus 4
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-12-03 Released: 2020-11-11 
• Deposition Author(s): Kremling, V., Loll, B., Osterrieder, N., Wahl, M., Dahmani, I., Chiantia, P., Azab, W.
• Funding Organization(s): German Research Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of glycoprotein D of equine alphaherpesviruses reveal potential binding sites to the entry receptor MHC-I.

Kremling, V., Loll, B., Pach, S., Dahmani, I., Weise, C., Wolber, G., Chiantia, S., Wahl, M.C., Osterrieder, N., Azab, W.

(2023) Front Microbiol 14: 1197120-1197120

• PubMed: 37250020 
• DOI: https://doi.org/10.3389/fmicb.2023.1197120
• Primary Citation Related Structures: 
  6SQJ, 6TM8


• PubMed Abstract: 
  

  Cell entry of most alphaherpesviruses is mediated by the binding of glycoprotein D (gD) to different cell surface receptors. Equine herpesvirus type 1 (EHV-1) and EHV-4 gDs interact with equine major histocompatibility complex I (MHC-I) to initiate entry into equine cells. We have characterized the gD-MHC-I interaction by solving the crystal structures of EHV-1 and EHV-4 gDs (gD1, gD4), performing protein-protein docking simulations, surface plasmon resonance (SPR) analysis, and biological assays. The structures of gD1 and gD4 revealed the existence of a common V-set immunoglobulin-like (IgV-like) core comparable to those of other gD homologs. Molecular modeling yielded plausible binding hypotheses and identified key residues (F213 and D261) that are important for virus binding. Altering the key residues resulted in impaired virus growth in cells, which highlights the important role of these residues in the gD-MHC-I interaction. Taken together, our results add to our understanding of the initial herpesvirus-cell interactions and will contribute to the targeted design of antiviral drugs and vaccine development.

---

Organizational Affiliation: 
• Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Berlin, Germany.
Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
Institute of Pharmacy (Pharmaceutical Chemistry), Freie Universität Berlin, Berlin, Germany.
Universität Potsdam, Institut für Biochemie und Biologie, Potsdam, Brandenburg, Germany.
BioSupraMol Core Facility, Bio-Mass Spectrometry, Freie Universität Berlin, Berlin, Germany.
Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany.
Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong SAR, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.39 kDa 
• Atom Count: 2,235 
• Modeled Residue Count: 244 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein D	A	332	Equid alphaherpesvirus 4	Mutation(s): 0  Gene Names: ORF72
UniProt
Find proteins for A0A0Y0A4Z5 (Equid alphaherpesvirus 4) Explore A0A0Y0A4Z5  Go to UniProtKB:  A0A0Y0A4Z5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36tm8

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.095	α = 90
b = 59.554	β = 90
c = 69.675	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Kremling, V., Loll, B., Osterrieder, N., Wahl, M., Dahmani, I., Chiantia, P., Azab, W.

---

Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary