7RA7 | pdb_00007ra7

Crystal structure of rabbit anti-HIV Fab 11A

• PDB DOI: https://doi.org/10.2210/pdb7RA7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Oryctolagus cuniculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-06-30 Released: 2022-07-06 
• Deposition Author(s): Oyen, D., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: in silico

Literature

Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions

Ozorowski, G., Cottrell, C.A., Oyen, D., de Val, N., Copps, J., Scaring, N., Polveroni, T.M., Wilson, I.A., Ward, A.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.32 kDa 
• Atom Count: 6,729 
• Modeled Residue Count: 864 
• Deposited Residue Count: 888 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
11A Fab heavy chain	A [auth H], C [auth A]	227	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
11A Fab light chain	B [auth L], D [auth B]	217	Oryctolagus cuniculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	I [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	E [auth L], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H], C [auth A]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.359	α = 90
b = 73.877	β = 97.82
c = 86.446	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Oyen, D., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI144462
Bill & Melinda Gates Foundation	United States	OPP1196345

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary