4M1G

Structure of murine IgG2a A27D7-Fab in complex with vaccinia antigen A33R at the resolution of 1.6 Angstroms

PDB DOI: https://doi.org/10.2210/pdb4M1G/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Vaccinia virus
Expression System: Mus musculus, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-08-02 Released: 2014-08-06
Deposition Author(s): Matho, M.H., Schlossman, A.M., Zajonc, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.226
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Literature

Structural and Functional Characterization of Anti-A33 Antibodies Reveal a Potent Cross-Species Orthopoxviruses Neutralizer.

Matho, M.H., Schlossman, A., Meng, X., Benhnia, M.R., Kaever, T., Buller, M., Doronin, K., Parker, S., Peters, B., Crotty, S., Xiang, Y., Zajonc, D.M.

(2015) PLoS Pathog 11: e1005148-e1005148

PubMed: 26325270 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1005148
Primary Citation of Related Structures:
4LQF, 4LU5, 4M1G

PubMed Abstract:
Vaccinia virus A33 is an extracellular enveloped virus (EEV)-specific type II membrane glycoprotein that is essential for efficient EEV formation and long-range viral spread within the host. A33 is a target for neutralizing antibody responses against EEV. In this study, we produced seven murine anti-A33 monoclonal antibodies (MAbs) by immunizing mice with live VACV, followed by boosting with the soluble A33 homodimeric ectodomain. Five A33 specific MAbs were capable of neutralizing EEV in the presence of complement. All MAbs bind to conformational epitopes on A33 but not to linear peptides. To identify the epitopes, we have adetermined the crystal structures of three representative neutralizing MAbs in complex with A33. We have further determined the binding kinetics for each of the three antibodies to wild-type A33, as well as to engineered A33 that contained single alanine substitutions within the epitopes of the three crystallized antibodies. While the Fab of both MAbs A2C7 and A20G2 binds to a single A33 subunit, the Fab from MAb A27D7 binds to both A33 subunits simultaneously. A27D7 binding is resistant to single alanine substitutions within the A33 epitope. A27D7 also demonstrated high-affinity binding with recombinant A33 protein that mimics other orthopoxvirus strains in the A27D7 epitope, such as ectromelia, monkeypox, and cowpox virus, suggesting that A27D7 is a potent cross-neutralizer. Finally, we confirmed that A27D7 protects mice against a lethal challenge with ectromelia virus.

Organizational Affiliation

Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.

Macromolecule Content

Total Structure Weight: 69.06 kDa
Atom Count: 5,015
Modelled Residue Count: 593
Deposited Residue Count: 629
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Murine IgG2a A27D7 Light chain Fab domain	A [auth L]	215	Mus musculus	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Murine IgG2a A27D7 Heavy chain Fab domain	B [auth H]	220	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A33R	C [auth A], D [auth B]	97	Vaccinia virus	Mutation(s): 4
UniProt
Find proteins for Q71TT1 (Vaccinia virus) Explore Q71TT1 Go to UniProtKB: Q71TT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q71TT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain F [auth L] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L]	E [auth L], F [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth L] Focus chain F [auth L] Interactions & Density Focus chain E [auth L] Focus chain F [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.226
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.019	α = 90
b = 95.019	β = 90
c = 127.332	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Matho, M.H.

Schlossman, A.M.

Zajonc, D.M.

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2015-09-23
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description