Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.34 kDa 
• Atom Count: 3470 
• Modelled Residue Count: 454 
• Deposited Residue Count: 454 
• Unique protein chains: 3

3F58

IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120 (MN ISOLATE); H315S MUTATION

• PDB DOI: 10.2210/pdb3F58/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1998-10-23 Released: 1999-02-09 
• Deposition Author(s): Stanfield, R.L., Cabezas, E., Satterthwait, A.C., Stura, E.A., Profy, A.T., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

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 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))	A [auth L]	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))	B [auth H]	228	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CYCLIC PEPTIDE (GP120))	C [auth P]	11	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.47	α = 90
b = 115.46	β = 90
c = 49.58	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-10-23 
• Released Date: 1999-02-09 
Deposition Author(s): Stanfield, R.L., Cabezas, E., Satterthwait, A.C., Stura, E.A., Profy, A.T., Wilson, I.A.

Revision History  

• 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