4E9O | pdb_00004e9o

Vaccinia D8L ectodomain structure

PDB DOI: https://doi.org/10.2210/pdb4E9O/pdb

Classification: VIRAL PROTEIN
Organism(s): Orthopoxvirus vaccinia
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-03-21 Released: 2012-06-06
Deposition Author(s): Matho, M.H., Zajonc, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.190 (Depositor), 0.195 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition by the Antibody LA5.

Matho, M.H., Maybeno, M., Benhnia, M.R., Becker, D., Meng, X., Xiang, Y., Crotty, S., Peters, B., Zajonc, D.M.

(2012) J Virol 86: 8050-8058

PubMed: 22623786 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JVI.00836-12
Primary Citation Related Structures:
4E9O, 4EBQ, 4ETQ

PubMed Abstract:
Smallpox vaccine is considered a gold standard of vaccines, as it is the only one that has led to the complete eradication of an infectious disease from the human population. B cell responses are critical for the protective immunity induced by the vaccine, yet their targeted epitopes recognized in humans remain poorly described. Here we describe the biochemical and structural characterization of one of the immunodominant vaccinia virus (VACV) antigens, D8, and its binding to the monoclonal antibody LA5, which is capable of neutralizing VACV in the presence of complement. The full-length D8 ectodomain was found to form a tetramer. We determined the crystal structure of the LA5 Fab-monomeric D8 complex at a resolution of 2.1 Å, as well as the unliganded structures of D8 and LA5-Fab at resolutions of 1.42 Å and 1.6 Å, respectively. D8 features a carbonic anhydrase (CAH) fold that has evolved to bind to the glycosaminoglycan (GAG) chondroitin sulfate (CS) on host cells. The central positively charged crevice of D8 was predicted to be the CS binding site by automated docking experiments. Furthermore, sequence alignment of various poxvirus D8 orthologs revealed that this crevice is structurally conserved. The D8 epitope is formed by 23 discontinuous residues that are spread across 80% of the D8 protein sequence. Interestingly, LA5 binds with a high-affinity lock-and-key mechanism above this crevice with an unusually large antibody-antigen interface, burying 2,434 Å(2) of protein surface.

Organizational Affiliation

Division of Cell Biology, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.

Macromolecule Content

Total Structure Weight: 32.84 kDa
Atom Count: 2,178
Modeled Residue Count: 230
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMV membrane protein	A [auth X]	269	Orthopoxvirus vaccinia	Mutation(s): 0 Gene Names: VACAC2_124, VACCL3_124, VAC_DPP17_124
UniProt
Find proteins for Q1M1K6 (Vaccinia virus) Explore Q1M1K6 Go to UniProtKB: Q1M1K6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1M1K6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain M [auth X] SDF format, chain L [auth X] SDF format, chain K [auth X] SDF format, chain J [auth X] SDF format, chain I [auth X] SDF format, chain H [auth X] SDF format, chain G [auth X] SDF format, chain F [auth X] SDF format, chain E [auth X] SDF format, chain D [auth X] SDF format, chain C [auth X] SDF format, chain B [auth X] MOL2 format, chain M [auth X] MOL2 format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain J [auth X] MOL2 format, chain I [auth X] MOL2 format, chain H [auth X] MOL2 format, chain G [auth X] MOL2 format, chain F [auth X] MOL2 format, chain E [auth X] MOL2 format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain B [auth X] mmCIF format, chain M [auth X] mmCIF format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain J [auth X] mmCIF format, chain I [auth X] mmCIF format, chain H [auth X] mmCIF format, chain G [auth X] mmCIF format, chain F [auth X] mmCIF format, chain E [auth X] mmCIF format, chain D [auth X] mmCIF format, chain C [auth X] mmCIF format, chain B [auth X]	B [auth X] C [auth X] D [auth X] E [auth X] F [auth X] B [auth X], C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], J [auth X], K [auth X], L [auth X], M [auth X]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.190 (Depositor), 0.195 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.174 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.281	α = 90
b = 71.281	β = 90
c = 44.415	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Matho, M.H.

Zajonc, D.M.

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2012-07-25
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description