3S5L

Crystal structure of CD4 mutant bound to HLA-DR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.234 

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This is version 1.2 of the entry. See complete history


Literature

Affinity maturation of human CD4 by yeast surface display and crystal structure of a CD4-HLA-DR1 complex.

Wang, X.X.Li, Y.Yin, Y.Mo, M.Wang, Q.Gao, W.Wang, L.Mariuzza, R.A.

(2011) Proc Natl Acad Sci U S A 108: 15960-15965

  • DOI: https://doi.org/10.1073/pnas.1109438108
  • Primary Citation of Related Structures:  
    3S4S, 3S5L

  • PubMed Abstract: 

    Helper T-cell activation generally requires the coreceptor CD4, which binds MHC class II molecules. A remarkable feature of the CD4-MHC class II interaction is its exceptionally low affinity, which ranges from K(D) = ∼200 μM to >2 mM. Investigating the biological role of the much lower affinity of this interaction than those of other cell-cell recognition molecules will require CD4 mutants with enhanced binding to MHC class II for testing in models of T-cell development. To this end, we used in vitro-directed evolution to increase the affinity of human CD4 for HLA-DR1. A mutant CD4 library was displayed on the surface of yeast and selected using HLA-DR1 tetramers or monomers, resulting in isolation of a CD4 clone containing 11 mutations. Reversion mutagenesis showed that most of the affinity increase derived from just two substitutions, Gln40Tyr and Thr45Trp. A CD4 variant bearing these mutations bound HLA-DR1 with K(D) = 8.8 μM, compared with >400 μM for wild-type CD4. To understand the basis for improved affinity, we determined the structure of this CD4 variant in complex with HLA-DR1 to 2.4 Å resolution. The structure provides an atomic-level description of the CD4-binding site on MHC class II and reveals how CD4 recognizes highly polymorphic HLA-DR, -DP, and -DQ molecules by targeting invariant residues in their α2 and β2 domains. In addition, the CD4 mutants reported here constitute unique tools for probing the influence of CD4 affinity on T-cell activation and development.


  • Organizational Affiliation

    W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA,
B [auth D]
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA
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PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen DR beta chainC [auth B],
D [auth E]
193Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
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PHAROS:  P01911
GTEx:  ENSG00000196126 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HA peptideE [auth C],
F
13Homo sapiensMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4
G, H
191Homo sapiensMutation(s): 4 
Gene Names: CD4
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Find proteins for P01730 (Homo sapiens)
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PHAROS:  P01730
GTEx:  ENSG00000010610 
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UniProt GroupP01730
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.2α = 90
b = 119.7β = 90
c = 137.4γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2011-09-21 
  • Deposition Author(s): Li, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary