6PEF | pdb_00006pef

Vaccine-elicited NHP FP-targeting antibody DF2F-a.01 in complex with HIV fusion peptide (residue 512-519)

• PDB DOI: https://doi.org/10.2210/pdb6PEF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca mulatta, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-06-20 Released: 2020-06-24 
• Deposition Author(s): Xu, K., Liu, K., Wang, Y., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Modular recognition of antigens provides a mechanism that improves vaccine-elicited antibody-class frequencies

Xu, K., Liu, K., Wang, Y., Kwong, P.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 94.34 kDa 
• Atom Count: 7,162 
• Modeled Residue Count: 875 
• Deposited Residue Count: 900 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody DF2F-a.01 heavy chain	A, D	226	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody DF2F-a.01 light chain	B, E	216	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV fusion peptide residue 512-519	C, F	8	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578  Go to UniProtKB:  P04578

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.574	α = 90
b = 52.504	β = 90.68
c = 151.716	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Xu, K., Liu, K., Wang, Y., Kwong, P.D.

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Refinement description, Structure summary