1R5I

Crystal structure of the MAM-MHC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex.

Zhao, Y.Li, Z.Drozd, S.J.Guo, Y.Mourad, W.Li, H.

(2004) Structure 12: 277-288

  • DOI: https://doi.org/10.1016/j.str.2004.01.008
  • Primary Citation of Related Structures:  
    1R5I

  • PubMed Abstract: 

    Mycoplasma arthritidis-derived mitogen (MAM) is a superantigen that can activate large fractions of T cells bearing particular TCR Vbeta elements. Here we report the crystal structure of MAM complexed with a major histocompatibility complex (MHC) antigen, HLA-DR1, loaded with haemagglutinin peptide 306-318 (HA). The structure reveals that MAM has a novel fold composed of two alpha-helical domains. This fold is entirely different from that of the pyrogenic superantigens, consisting of a beta-grasped motif and a beta barrel. In the complex, the N-terminal domain of MAM binds orthogonally to the MHC alpha1 domain and the bound HA peptide, and to a lesser extent to the MHC beta1 domain. Two MAM molecules form an asymmetric dimer and cross-link two MHC antigens to form a plausible, dimerized MAM-MHC complex. These data provide the first crystallographic evidence that superantigens can dimerize MHC molecules. Based on our structure, a model of the TCR2MAM2MHC2 complex is proposed.


  • Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Empire State Plaza, PO Box 509, Albany, NY 12201, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain
A, E
181Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chain
B, F
190Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
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Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin peptide
C, G
13N/AMutation(s): 0 
UniProt
Find proteins for P11133 (Influenza A virus (strain A/Swine/Hong Kong/81/1978 H3N2))
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UniProt GroupP11133
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
superantigen
D, H
216Metamycoplasma arthritidisMutation(s): 0 
UniProt
Find proteins for Q48898 (Metamycoplasma arthritidis)
Explore Q48898 
Go to UniProtKB:  Q48898
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UniProt GroupQ48898
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.286α = 90
b = 178.814β = 90
c = 179.554γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
CCP4data scaling
AMoREphasing
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-30
    Changes: Structure summary