7RPT | pdb_00007rpt

Crystal Structure of Protective Human Antibody 3A6 Fab Against Ebola Virus

• PDB DOI: https://doi.org/10.2210/pdb7RPT/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: in silico

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 188.18 kDa 
• Atom Count: 13,390 
• Modeled Residue Count: 1,720 
• Deposited Residue Count: 1,748 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3A6 Fab heavy chain	A, C, E, G	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3A6 Fab light chain	B, D, F, H	219	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.659	α = 98.737
b = 65.674	β = 91.366
c = 125.556	γ = 96.009

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
STARANISO	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Salie, Z.L., Saphire, E.O., Davis, C.W., Ahmed, R.

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

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary