8V5P

Crystal Structure of the C-terminal domain of the VZV gE ectodomain in complex with the Fab of human antibody 5A2

PDB DOI: https://doi.org/10.2210/pdb8V5P/pdb

Classification: VIRAL PROTEIN
Organism(s): Human alphaherpesvirus 3, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-11-30 Released: 2024-10-09
Deposition Author(s): Harshbarger, W., Malito, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.33 Å
R-Value Free: 0.272
R-Value Work: 0.222
R-Value Observed: 0.225

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structures of the Varicella Zoster Virus Glycoprotein E and Epitope Mapping of Vaccine-Elicited Antibodies

Harshbarger, W.D., Holzapfel, G., Seraj, N., Tian, S., Chesterman, C., Fu, Z., Pan, Y., Harelson, C., Peng, D., Huang, Y., Chandramouli, S., Malito, E., Bottomley, M.J., Williams, J.

(2024) Vaccines (Basel) 12

DOI: https://doi.org/10.3390/vaccines12101111

Macromolecule Content

Total Structure Weight: 306.1 kDa
Atom Count: 18,368
Modelled Residue Count: 2,396
Deposited Residue Count: 2,824
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein E	A, D, G, J [auth C]	254	Human alphaherpesvirus 3	Mutation(s): 0 Gene Names: ORF68
UniProt
Find proteins for A0A1B1JEP3 (Human herpesvirus 3) Explore A0A1B1JEP3 Go to UniProtKB: A0A1B1JEP3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1B1JEP3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5A2 Fab heavy chain	B [auth H], E, H [auth J], K [auth F]	242	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5A2 Fab Light Chain	C [auth L], F [auth Y], I [auth X], L [auth I]	210	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.33 Å
R-Value Free: 0.272
R-Value Work: 0.222
R-Value Observed: 0.225
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 274.822	α = 90
b = 274.822	β = 90
c = 128.957	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SERGUI	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Harshbarger, W.

Funding Organization	Location	Grant Number
Not funded	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.