PDBsum entry: 3c2a

Immune system

PDB-id: 3c2a

Main view

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

216 a.a. *

231 a.a. *

13 a.a. *

Waters ×187

* Residue conservation analysis

Tools

Clefts Calculation

Bottom view	Right view

PDB id:

3c2a

Name:

Immune system

Title:

Antibody fab fragment 447-52d in complex with ug1033 peptide

Structure:

Lambda-chain. Chain: l, m. Fab 447-52d, heavy chain. Chain: h, i. Envelope glycoprotein. Chain: p, q. Engineered: yes

Source:

Homo sapiens. Human. Synthetic: yes. Other_details: the peptide is naturally found in HIV-1 gp120.

UniProt:

Chains P, Q: Q9YWB6 (Q9YWB6_9HIV1)

Seq:

109 a.a.

Struc:

13 a.a.

Key:

PfamA domain

Secondary structure

Resolution:

2.10Å

R-factor:

0.241

R-free:

0.298

Authors:

A.K.Dhillon,R.L.Stanfield,I.A.Wilson

Key ref:

A.K.Dhillon et al. (2008). Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set.. Acta Crystallogr D Biol Crystallogr, 64, 792-802. [PubMed id: 18566514] [DOI: 10.1107/S0907444908013978]

Date:

24-Jan-08

Release date:

08-Jul-08

Related entries:

1q1j
447-52d in complex with v3 peptide

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1107/S0907444908013978

Acta Crystallogr D Biol Crystallogr 64:792-802 (2008)

PubMed id: 18566514

Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set.

A.K.Dhillon, R.L.Stanfield, M.K.Gorny, C.Williams, S.Zolla-Pazner, I.A.Wilson.

ABSTRACT

Although antibodies against the third variable loop (V3) of the HIV-1 viral envelope glycoprotein are among the first neutralizing antibodies to be detected in infected individuals, they are normally restricted in their specificity. X-ray crystallographic studies of V3-specific antibodies have contributed to a more thorough understanding of recognition of this epitope and of conserved features in the V3 loop that could potentially aid in the design of a multi-component vaccine. The human antibody 447-52D exhibits relatively broad neutralization of primary viral isolates compared with other V3-loop antibodies. A crystal structure of Fab 447-52D in complex with a V3 peptide (UG1033) was determined at 2.1 angstroms resolution. The structure was determined using an epitaxially twinned data set and in-house programs to detect and remove overlapping reflections. Although the processed data have lower than desired completeness and slightly higher than normal R values for the resolution, good-quality electron-density maps were obtained that enabled structure determination. The structure revealed an extended CDR H3 loop that forms a beta-sheet with the peptide, with the predominant contacts being main-chain hydrogen bonds. The V3 peptide and Fab show high structural homology with the previously reported structures of other Fab 447-52D complexes, reinforcing the idea that the V3 loop may adopt a small set of conserved structures, particularly around the crown of the beta-hairpin.