6PDU | pdb_00006pdu

Vaccine-elicited NHP FP-targeting antibody 13N024-a.01 in complex with HIV fusion peptide (residue 512-519)

PDB DOI: https://doi.org/10.2210/pdb6PDU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, 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: 1.95 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

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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: 47.41 kDa
Atom Count: 3,727
Modeled Residue Count: 443
Deposited Residue Count: 443
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 13N024-a.01, light chain	A [auth L]	219	Homo sapiens	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 13N024-a.01, heavy chain	B [auth H]	216	Homo sapiens	Mutation(s): 0 Gene Names: HEL-214

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 fusion peptide residue 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
Entity Groups
UniProt Group	P04578
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.174 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.032	α = 90
b = 74.203	β = 90
c = 93.914	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

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Entry History

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-24
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.