8D01

The domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13

• PDB DOI: https://doi.org/10.2210/pdb8D01/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Macaca mulatta
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-05-25 Released: 2023-12-13 
• Deposition Author(s): Xian, Y., Wilson, I.A.
• Funding Organization(s): International AIDS Vaccine Initiative, Consortia for HIV/AIDS Vaccine Development, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.229 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Structural and Antigenic Characterization of B Cell Mosaic Env Trimers

Xian, Y., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 95.56 kDa 
• Atom Count: 6,980 
• Modelled Residue Count: 855 
• Deposited Residue Count: 876 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
21N13 Fab heavy chain	A [auth H], C [auth A]	225	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
21N13 Fab light chain	B [auth L], D [auth B]	213	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.229 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 260.367	α = 90
b = 45.151	β = 98.609
c = 84.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Xian, Y., Wilson, I.A.

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Funding Organization	Location	Grant Number
International AIDS Vaccine Initiative	United States	INV-008352/OPP1153692
Consortia for HIV/AIDS Vaccine Development	United States	CHAVD 1UM1 AI144462
Other private		P01 AI110657

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Database references, Structure summary