6P8D | pdb_00006p8d

Vaccine-elicited murine FP-targeting antibody vFP6.01 in complex with HIV fusion peptide (residue 512-519)

PDB DOI: https://doi.org/10.2210/pdb6P8D/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Human immunodeficiency virus 1
Mutation(s): No

Deposited: 2019-06-07 Released: 2020-06-10
Deposition Author(s): Xu, K., Liu, K., Wang, Y., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.309 (Depositor), 0.310 (DCC)
R-Value Work:
0.271 (Depositor), 0.280 (DCC)
R-Value Observed:
0.272 (Depositor)

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

Total Structure Weight: 97.23 kDa
Atom Count: 6,824
Modeled Residue Count: 869
Deposited Residue Count: 890
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 VFP6.01 heavy chain	A, C [auth D]	218	Mus musculus	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 VFP6.01 light chain	B, D [auth E]	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: Sequence | 3D Structure

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.309 (Depositor), 0.310 (DCC)
R-Value Work: 0.271 (Depositor), 0.280 (DCC)
R-Value Observed: 0.272 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.311	α = 90
b = 119.777	β = 90
c = 185.503	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

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Entry History

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-10
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.