3GO1 | pdb_00003go1

Crystal structure of anti-HIV-1 Fab 268-D in complex with V3 peptide MN

PDB DOI: https://doi.org/10.2210/pdb3GO1/pdb

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

Deposited: 2009-03-18 Released: 2010-06-23
Deposition Author(s): Kong, X.P., Burke, V.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.213 (Depositor), 0.215 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Conserved structural elements in the V3 crown of HIV-1 gp120.

Jiang, X., Burke, V., Totrov, M., Williams, C., Cardozo, T., Gorny, M.K., Zolla-Pazner, S., Kong, X.P.

(2010) Nat Struct Mol Biol 17: 955-961

PubMed: 20622876 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1861
Primary Citation Related Structures:
3GO1, 3MLR, 3MLS, 3MLT, 3MLU, 3MLV, 3MLW, 3MLX, 3MLY, 3MLZ

PubMed Abstract:
Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserved elements could serve as epitopes to be targeted by a vaccine against HIV-1. Here we perform a systematic structural analysis of representative human anti-V3 monoclonal antibodies in complex with V3 peptides, revealing that the crown of V3 has four conserved structural elements: an arch, a band, a hydrophobic core and the peptide backbone. These are either unaffected by or are subject to minimal sequence variation. As these regions are targeted by cross-clade neutralizing human antibodies, they provide a blueprint for the design of vaccine immunogens that could elicit broadly cross-reactive protective antibodies.

Organizational Affiliation

Department of Biochemistry, New York University School of Medicine, New York, New York, USA.

Macromolecule Content

Total Structure Weight: 48.19 kDa
Atom Count: 3,735
Modeled Residue Count: 445
Deposited Residue Count: 445
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 268-D, light chain	A [auth L]	209	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 268-D, heavy chain	B [auth H]	222	Homo sapiens	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	C [auth P]	14	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN)) Explore P05877 Go to UniProtKB: P05877
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05877
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 H SDF format, chain G [auth H] SDF format, chain F [auth H] SDF format, chain E [auth L] SDF format, chain D [auth L] MOL2 format, chain H MOL2 format, chain G [auth H] MOL2 format, chain F [auth H] MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] mmCIF format, chain H mmCIF format, chain G [auth H] mmCIF format, chain F [auth H] mmCIF format, chain E [auth L] mmCIF format, chain D [auth L]	D [auth L], E [auth L], F [auth H], G [auth H], H	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth H] Focus chain G [auth H] Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.213 (Depositor), 0.215 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.377	α = 90
b = 69.26	β = 107.24
c = 71.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
DENZO	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-06-23

Deposition Author(s):

Kong, X.P.

Burke, V.J.

Revision History (Full details and data files)

Version 1.0: 2010-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description, Source and taxonomy
Version 1.3: 2019-07-24
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary