6P60

Vaccine-elicited NHP FP-targeting neutralizing antibody A12V163-a.02 in complex with HIV fusion peptide (residue 512-519)

PDB DOI: https://doi.org/10.2210/pdb6P60/pdb

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

Deposited: 2019-05-31 Released: 2020-06-03
Deposition Author(s): Xu, K., Liu, K., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.209
R-Value Work: 0.197
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Vaccine-elicited NHP FP-targeting neutralizing antibody A12V163-a.02 in complex with HIV fusion peptide (residue 512-519)

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

To be published.

Macromolecule Content

Total Structure Weight: 189.21 kDa
Atom Count: 14,008
Modelled Residue Count: 1,750
Deposited Residue Count: 1,780
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody A12V163-a.02 heavy chain	A, D [auth C], G, J	225	Platyrrhini	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody A12V163-a.02 light chain	B, E [auth D], H, K	212	Platyrrhini	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV fusion peptide residue 512-519	C [auth E], F, I, L	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
Entity Groups
UniProt Group	P04578
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.209
R-Value Work: 0.197
R-Value Observed: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.784	α = 90
b = 72.199	β = 96.63
c = 185.526	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.