2F58

IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120) (MN ISOLATE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

Starting Model: experimental
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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

  • 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. We have determined three crystal structures of Fab 58.2, a broadly neutralizing antibody, in complex with one linear and two cyclic peptides the amino acid sequence of which comes from the MN isolate of the gp120 V3 loop. Although the peptide conformations are very similar for the linear and cyclic forms, they differ from that seen for the identical peptide bound to a different broadly neutralizing antibody, Fab 59.1, and for a similar peptide bound to the MN-specific Fab 50.1. The conformational difference in the peptide is localized around residues Gly-Pro-Gly-Arg, which are highly conserved in different HIV-1 isolates and are predicted to adopt a type II beta turn. The V3 loop can adopt at least two different conformations for the highly conserved Gly-Pro-Gly-Arg sequence at the tip of the loop. Thus, the HIV-1 V3 loop has some inherent conformational flexibility that may relate to its biological function.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN))A [auth L]216Mus musculusMutation(s): 0 
UniProt
Find proteins for P01666 (Mus musculus)
Explore P01666 
Go to UniProtKB:  P01666
Entity Groups  
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UniProt GroupP01666
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN))B [auth H]228Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (HIV-1 GP120)C [auth P]11N/AMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARN
Query on ARN

Download Ideal Coordinates CCD File 
D [auth P]1-IMINO-5-PENTANONE
C5 H9 N O
UWHJGSVKWBLVLI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.08α = 90
b = 114.72β = 90
c = 49.53γ = 90
Software Package:
Software NamePurpose
UCSD-systemdata collection
UCSD-systemdata reduction
MERLOTphasing
X-PLORmodel building
X-PLORrefinement
UCSD-systemdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-09
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description