1F58

IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 24-RESIDUE PEPTIDE (RESIDUES 308-333 OF HIV-1 GP120 (MN ISOLATE) WITH ALA TO AIB SUBSTITUTION AT POSITION 323

PDB DOI: https://doi.org/10.2210/pdb1F58/pdb

Classification: Viral protein/Immune system
Organism(s): Mus musculus, HIV-1 M:B_MN
Mutation(s): No

Deposited: 1998-10-21 Released: 1999-02-02
Deposition Author(s): Stanfield, R.L., Cabezas, E., Satterthwait, A.C., Stura, E.A., Profy, A.T., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.256
R-Value Work: 0.196
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.

Stanfield, R., Cabezas, E., Satterthwait, A., Stura, E., Profy, A., Wilson, I.

(1999) Structure 7: 131-142

PubMed: 10368281 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(99)80020-3
Primary Citation of Related Structures:
1F58, 2F58, 3F58

PubMed Abstract:
The third hypervariable (V3) loop of HIV-1 gp120 has been termed the principal neutralizing determinant (PND) of the virus and is involved in many aspects of virus infectivity. The V3 loop is required for viral entry into the cell via membrane fusion and is believed to interact with cell surface chemokine receptors on T cells and macrophages. Sequence changes in V3 can affect chemokine receptor usage, and can, therefore, modulate which types of cells are infected. Antibodies raised against peptides with V3 sequences can neutralize laboratory-adapted strains of the virus and inhibit syncytia formation. Fab fragments of these neutralizing antibodies in complex with V3 loop peptides have been studied by X-ray crystallography to determine the conformation of the V3 loop.

Organizational Affiliation

The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla CA 92037, USA.

Macromolecule Content

Total Structure Weight: 51.16 kDa
Atom Count: 3,617
Modelled Residue Count: 455
Deposited Residue Count: 467
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IGG1 ANTIBODY 58.2 (LIGHT CHAIN))	A [auth L]	216	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01666 (Mus musculus) Explore P01666 Go to UniProtKB: P01666
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01666
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IGG1 ANTIBODY 58.2 (HEAVY CHAIN))	B [auth H]	228	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q99LC4 (Mus musculus) Explore Q99LC4 Go to UniProtKB: Q99LC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99LC4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	C [auth P]	23	HIV-1 M:B_MN	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	C [auth P]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.256
R-Value Work: 0.196
R-Value Observed: 0.196
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.89	α = 90
b = 71.91	β = 98.31
c = 88.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MERLOT	phasing
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1999-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-02-02
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-08-22
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.4: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description