1JL4

CRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL TWO DOMAIN FRAGMENT COMPLEXED TO A CLASS II MHC MOLECULE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.453 
  • R-Value Work: 0.420 
  • R-Value Observed: 0.428 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the human CD4 N-terminal two-domain fragment complexed to a class II MHC molecule.

Wang, J.H., Meijers, R., Xiong, Y., Liu, J.H., Sakihama, T., Zhang, R., Joachimiak, A., Reinherz, E.L.

(2001) Proc Natl Acad Sci U S A 98: 10799-10804

  • DOI: 10.1073/pnas.191124098
  • Primary Citation of Related Structures:  
    1JL4

  • PubMed Abstract: 

    • The structural basis of the interaction between the CD4 coreceptor and a class II major histocompatibility complex (MHC) is described. The crystal structure of a complex containing the human CD4 N-terminal two-domain fragment and the murine I-A(k) class II MHC molecule with associated peptide (pMHCII) shows that only the "top corner" of the CD4 molecule directly contacts pMHCII ...

    The structural basis of the interaction between the CD4 coreceptor and a class II major histocompatibility complex (MHC) is described. The crystal structure of a complex containing the human CD4 N-terminal two-domain fragment and the murine I-A(k) class II MHC molecule with associated peptide (pMHCII) shows that only the "top corner" of the CD4 molecule directly contacts pMHCII. The CD4 Phe-43 side chain extends into a hydrophobic concavity formed by MHC residues from both alpha 2 and beta 2 domains. A ternary model of the CD4-pMHCII-T-cell receptor (TCR) reveals that the complex appears V-shaped with the membrane-proximal pMHCII at the apex. This configuration excludes a direct TCR-CD4 interaction and suggests how TCR and CD4 signaling is coordinated around the antigenic pMHCII complex. Human CD4 binds to HIV gp120 in a manner strikingly similar to the way in which CD4 interacts with pMHCII. Additional contacts between gp120 and CD4 give the CD4-gp120 complex a greater affinity. Thus, ligation of the viral envelope glycoprotein to CD4 occludes the pMHCII-binding site on CD4, contributing to immunodeficiency.

    Organizational Affiliation: 

    Laboratory of Immunobiology and Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA. jwang@dfci.harvard.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K ALPHA CHAINA178Mus musculusMutation(s): 0 
Gene Names: H2-Aa
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Find proteins for P01910 (Mus musculus)
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UniProt GroupP01910
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K BETA CHAINB185Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for P06343 (Mus musculus)
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UniProt GroupP06343
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
OVOTRANSFERRINC16Gallus gallusMutation(s): 0 
UniProt
Find proteins for P02789 (Gallus gallus)
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UniProt GroupP02789
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL SURFACE GLYCOPROTEIN CD4D178Homo 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 
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UniProt GroupP01730
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.453 
  • R-Value Work: 0.420 
  • R-Value Observed: 0.428 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.195α = 90
b = 145.195β = 90
c = 103.846γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
EPMRphasing
FFFEARmodel building
REFMACrefinement
FFFEARphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-19
    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