7D5Z | pdb_00007d5z

Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8

• PDB DOI: https://doi.org/10.2210/pdb7D5Z/pdb

• Classification: VIRAL PROTEIN
• Organism(s): human gammaherpesvirus 4, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-09-28 Released: 2021-10-20 
• Deposition Author(s): Zhu, Q., Shan, S., Yu, J., Wang, X., Zhang, L., Zeng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

A Neutralizing Antibody Targeting a New Site of Vulnerability on Epstein-Barr Virus gH/gL Protects against Dual-Tropic Infection

Zhu, Q., Shan, S., Yu, J., Wang, X., Zhang, L., Zeng, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 653.99 kDa 
• Atom Count: 36,304 
• Modeled Residue Count: 4,704 
• Deposited Residue Count: 5,920 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	A [auth M], E [auth A], I [auth E], M [auth I]	665	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: gH, BXLF2
UniProt
Find proteins for Q3KSQ3 (Epstein-Barr virus (strain GD1)) Explore Q3KSQ3  Go to UniProtKB:  Q3KSQ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	B [auth N], F [auth B], J [auth F], N [auth J]	112	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: gL, BKRF2
UniProt
Find proteins for Q3KSS3 (Epstein-Barr virus (strain GD1)) Explore Q3KSS3  Go to UniProtKB:  Q3KSS3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 1D8	C [auth O], G [auth C], K [auth G], O [auth K]	233	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 1D8	D [auth P], H [auth D], L [auth H], P [auth L]	470	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.277 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.865	α = 90
b = 212.865	β = 90
c = 598.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-20 
Deposition Author(s): Zhu, Q., Shan, S., Yu, J., Wang, X., Zhang, L., Zeng, M.

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary