3LQA | pdb_00003lqa

Crystal structure of clade C gp120 in complex with sCD4 and 21c Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.322 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.241 (DCC) 

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This is version 1.6 of the entry. See complete history

Literature

Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity.

Diskin, R.Marcovecchio, P.M.Bjorkman, P.J.

(2010) Nat Struct Mol Biol 17: 608-613

  • DOI: https://doi.org/10.1038/nsmb.1796
  • Primary Citation Related Structures: 
    3LMJ, 3LQA

  • PubMed Abstract: 

    Strategies to combat HIV-1 require structural knowledge of envelope proteins from viruses in HIV-1 clade C, the most rapidly spreading subtype in the world. We present a crystal structure containing a clade C gp120 envelope. The structure, a complex between gp120, the host receptor CD4 and the CD4-induced antibody 21c, reveals that the 21c epitope involves contacts with gp120, a nonself antigen, and with CD4, an autoantigen. Binding studies using wild-type and mutant CD4 show that 21c Fab binds CD4 in the absence of gp120, and that binding of 21c to clade C and HIV-2 gp120s requires the crystallographically observed 21c-CD4 interaction. Additional binding data suggest a role for the gp120 V1V2 loop in creating a high-affinity, but slow-forming, epitope for 21c after CD4 binds. These results contribute to a molecular understanding of CD4-induced antibodies and provide the first visualization to our knowledge of a potentially autoreactive antibody Fab complexed with both self and nonself antigens.


  • Organizational Affiliation
    • Division of Biology, California Institute of Technology, Pasadena, California, USA.

Macromolecule Content 

  • Total Structure Weight: 106.59 kDa 
  • Atom Count: 6,945 
  • Modeled Residue Count: 903 
  • Deposited Residue Count: 972 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4A [auth C]192Homo sapiensMutation(s): 0 
Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens)
Explore P01730 
Go to UniProtKB:  P01730
PHAROS:  P01730
GTEx:  ENSG00000010610 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01730
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B [auth G]332Human immunodeficiency virus 1Mutation(s): 7 
Gene Names: env
UniProt
Find proteins for Q1PHM6 (Human immunodeficiency virus type 1)
Explore Q1PHM6 
Go to UniProtKB:  Q1PHM6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1PHM6
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of anti HIV Fab from human 21c antibodyC [auth H]231Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of anti HIV Fab from human 21c antibodyD [auth L]217Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.322 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.241 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.73α = 90
b = 187.93β = 90
c = 151.67γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2021-10-13
    Changes: Database references, Structure summary
  • Version 1.6: 2024-10-30
    Changes: Data collection, Structure summary