7RPU | pdb_00007rpu

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
Modeled 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.