6X78

Vaccine-elicited mouse FP-targeting neutralizing antibody vFP48.03 in complex with HIV fusion peptide (residue 512-519)

PDB DOI: https://doi.org/10.2210/pdb6X78/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Mus musculus, Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-05-29 Released: 2021-06-02
Deposition Author(s): Xu, K., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.226
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Distinct Classes of HIV-1 Cross-Clade Neutralizing Antibodies Targeting Fusion Peptide Elicited in Mice by Diverse Immunization Regimens

Xu, K., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 100 kDa
Atom Count: 7,264
Modelled Residue Count: 887
Deposited Residue Count: 922
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody vFP48.03 light chain	A, D [auth L]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody vFP48.03 heavy chain	B, C [auth H]	234	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV fusion peptide 512-519 V2	E [auth G], F [auth I]	8	Human immunodeficiency virus 1	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L]	G [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.226
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.993	α = 90
b = 92.733	β = 90
c = 143.424	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-02
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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.