7RPU

Crystal Structure of Protective Human Antibody 3A6 Fab Against Ebola Virus with GP Stalk/MPER Epitope Peptide

PDB DOI: https://doi.org/10.2210/pdb7RPU/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens, Ebola virus - Eckron (Zaire, 1976)
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-08-04 Released: 2022-07-13
Deposition Author(s): Salie, Z.L., Saphire, E.O., Davis, C.W., Ahmed, R.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.160 (Depositor), 0.160 (DCC)
R-Value Work:
0.141 (Depositor), 0.140 (DCC)
R-Value Observed:
0.142 (Depositor)

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

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

Literature

Protection against Ebola virus disease and neutralization mechanism of a survivor's anti-stalk-MPER antibody

Salie, Z.L., Saphire, E.O.

To be published.

Macromolecule Content

Total Structure Weight: 48.76 kDa
Atom Count: 4,049
Modelled Residue Count: 441
Deposited Residue Count: 452
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3A6 Fab heavy chain	A	218	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3A6 Fab light chain	B	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GP2 epitope peptide	C [auth P]	15	Ebola virus - Eckron (Zaire, 1976)	Mutation(s): 0
UniProt
Find proteins for P87671 (Zaire ebolavirus (strain Eckron-76)) Explore P87671 Go to UniProtKB: P87671
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P87671
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.160 (Depositor), 0.160 (DCC)
R-Value Work: 0.141 (Depositor), 0.140 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.293	α = 90
b = 66.427	β = 104.24
c = 67.981	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-07-13
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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.