3C2A

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

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This is version 1.2 of the entry. See complete history. 


Literature

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

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

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

  • DOI: 10.1107/S0907444908013978
  • Primary Citation of Related Structures:  
    3C2A

  • 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 crystallographi ...

    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.

    Organizational Affiliation: 

    Department of Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 447-52D light chain L, M216Homo sapiensMutation(s): 0 
Gene Names: IGLC2
Find proteins for P0DOY2 (Homo sapiens)
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Go to UniProtKB:  P0DOY2
NIH Common Fund Data Resources
GTEx:  ENSG00000211677
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 447-52D heavy chain H, I231Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein P, Q13Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q9YWB6 (Human immunodeficiency virus 1)
Explore Q9YWB6 
Go to UniProtKB:  Q9YWB6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.251α = 90
b = 76.482β = 101.49
c = 114.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-05-09
    Changes: Advisory, Data collection, Source and taxonomy, Structure summary