1YMM

TCR/HLA-DR2b/MBP-peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.318 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.274 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.276 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.5 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: https://doi.org/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 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
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain191Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
Entity Groups  
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UniProt GroupP01903
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01903-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR beta chain198Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
Explore P01911 
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
MBP peptide23Homo sapiensMutation(s): 0 
Gene Names: MBP
UniProt & NIH Common Fund Data Resources
Find proteins for P02686 (Homo sapiens)
Explore P02686 
Go to UniProtKB:  P02686
PHAROS:  P02686
GTEx:  ENSG00000197971 
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UniProt GroupP02686
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha chain207Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
Entity Groups  
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UniProt GroupP01848
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor beta chain249Homo sapiensMutation(s): 2 
UniProt
Find proteins for P01850 (Homo sapiens)
Explore P01850 
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UniProt GroupP01850
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.318 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.274 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.276 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2021-10-20
    Changes: Advisory, Database references, Structure summary
  • Version 1.5: 2024-11-20
    Changes: Data collection, Structure summary