1YMM

TCR/HLA-DR2b/MBP-peptide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


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


Literature

Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor.

Hahn, M., Nicholson, M.J., Pyrdol, J., Wucherpfennig, K.W.

(2005) Nat Immunol 6: 490-496

  • DOI: 10.1038/ni1187
  • Primary Citation of Related Structures:  
    1YMM

  • PubMed Abstract: 

    • Autoimmune diseases are caused by self-reactive lymphocytes that have escaped deletion. Here we have determined the structure of the trimolecular complex for a T cell receptor (TCR) from a patient with multiple sclerosis that causes autoimmunity in t ...

    Autoimmune diseases are caused by self-reactive lymphocytes that have escaped deletion. Here we have determined the structure of the trimolecular complex for a T cell receptor (TCR) from a patient with multiple sclerosis that causes autoimmunity in transgenic mice. The structure showed a TCR topology notably different from that of antimicrobial TCRs. Rather than being centered on the peptide-major histocompatibility complex, this TCR contacted only the N-terminal peptide segment and made asymmetrical interactions with the major histocompatibility complex helices. The interaction was dominated by the hypervariable complementarity-determining region 3 loops, indicating that unconventional topologies are possible because of the unique complementarity-determining region 3 sequences created during rearrangement. This topology reduces the interaction surface with peptide and alters the geometry for CD4 association. We propose that unusual TCR-binding properties can permit autoreactive T cells to escape deletion.

    Organizational Affiliation: 

    Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA191Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
GTEx  ENSG00000204287
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR beta chainB198Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
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PHAROS  P01911
GTEx  ENSG00000196126
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MBP peptideC23N/AMutation(s): 0 
Find proteins for P02686 (Homo sapiens)
Explore P02686 
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PHAROS  P02686
GTEx  ENSG00000197971
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T cell receptor alpha chainD207Homo sapiensMutation(s): 0 
Gene Names: TRAC, TCRA
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
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PHAROS  P01848
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor beta chainE249Homo sapiensMutation(s): 2 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.34α = 90
b = 212.62β = 90
c = 278.22γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary