6PDS

Vaccine-elicited NHP FP-targeting antibody 0PV-a.04 in complex with HIV fusion peptide (residue 512-519)

• PDB DOI: https://doi.org/10.2210/pdb6PDS/pdb

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


• Deposited: 2019-06-19 Released: 2020-06-24 
• Deposition Author(s): Xu, K., Liu, K., Wang, Y., Kwong, P.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

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 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 95.61 kDa 
• Atom Count: 7,418 
• Modelled Residue Count: 877 
• Deposited Residue Count: 880 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 0PV-a.04 light chain	A, D [auth L]	212	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 0PV-a.04 heavy chain	B, C [auth H]	220	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 fusion peptide residue 512-519	E [auth G], F [auth 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth B], I [auth H], J [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.857	α = 90
b = 74.381	β = 90
c = 187.198	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