6P7H

Vaccine-elicited NHP FP-targeting neutralizing antibody DF2F-b.04 in complex with HIV fusion peptide (residue 512-519)

• PDB DOI: https://doi.org/10.2210/pdb6P7H/pdb

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


• Deposited: 2019-06-05 Released: 2020-06-10 
• Deposition Author(s): Xu, K., Liu, K., Wang, Y., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.230 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

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

Macromolecule Content

• Total Structure Weight: 48.8 kDa 
• Atom Count: 3,664 
• Modelled Residue Count: 437 
• Deposited Residue Count: 453 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody DF2F-b.04 light chain	A [auth B]	219	Platyrrhini	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody DF2F-b.04 heavy chain	B [auth A]	226	Platyrrhini	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV fusion peptide residues (512-519)	C	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: 1.78 Å
• R-Value Free: 0.230 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.164	α = 90
b = 62.219	β = 90
c = 136.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Xu, K., Liu, K., Wang, Y., Kwong, P.D.

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release