3C2A

Antibody Fab fragment 447-52D in complex with UG1033 peptide

Summary for 3C2A

• Entry DOI: 10.2210/pdb3c2a/pdb
• Related: 1q1j
• Descriptor: Fab 447-52D light chain, Fab 447-52D heavy chain, Envelope glycoprotein, ... (4 entities in total)
• Functional Keywords: antibody fab hiv-1 peptide, envelope protein, immune system
• Biological source: Homo sapiens (human); More
• Cellular location: Virion membrane : Q9YWB6
• Total number of polymer chains: 6
• Total formula weight: 97941.36

Authors

Dhillon, A.K.,Stanfield, R.L.,Wilson, I.A. (deposition date: 2008-01-24, release date: 2008-07-08, Last modification date: 2023-08-30)

Primary citation

Dhillon, A.K.,Stanfield, R.L.,Gorny, M.K.,Williams, C.,Zolla-Pazner, S.,Wilson, I.A.
Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set
Acta Crystallogr.,Sect.D, 64:792-802, 2008

PubMed 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.

PubMed: 18566514
DOI: 10.1107/S0907444908013978

Experimental method

X-RAY DIFFRACTION (2.1 Å)