3MBE

TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

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This is version 2.0 of the entry. See complete history


Literature

The diabetogenic mouse MHC class II molecule I-Ag7 is endowed with a switch that modulates TCR affinity.

Yoshida, K.Corper, A.L.Herro, R.Jabri, B.Wilson, I.A.Teyton, L.

(2010) J Clin Invest 120: 1578-1590

  • DOI: 10.1172/JCI41502
  • Primary Citation of Related Structures:  
    3MBE

  • PubMed Abstract: 
  • Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-Ag7, typically have a small, uncharged amino acid residue at position 57 of their beta chain (beta57); this results in the absence of a salt bridge between beta57 and Argalpha76, which is adjacent to the P9 pocket of the peptide-binding groove ...

    Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-Ag7, typically have a small, uncharged amino acid residue at position 57 of their beta chain (beta57); this results in the absence of a salt bridge between beta57 and Argalpha76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Argalpha76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3beta. The crystal structure of one such TCR in complex with I-Ag7 bound to a peptide containing a neutral P9 residue revealed that a network of favorable long-range (greater than 4 A) electrostatic interactions existed among Argalpha76, the neutral P9 residue, and TCR, which supported the substantially increased TCR/peptide-MHC affinity. This network could be modulated or switched to a lower affinity interaction by the introduction of a negative charge at position P9 of the peptide. Our results support the existence of a switch at residue beta57 of the I-Ag7 and HLA-DQ8 class II molecules and potentially link normal thymic TCR selection with abnormal peripheral behavior.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II H2-IAg7 ALPHA CHAINA,
F [auth E]
190Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus)
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UniProt GroupP04228
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II H2-IAg7 BETA CHAINB,
G [auth F]
201Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
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UniProt GroupQ31135
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE HEL 11-27C [auth P],
H [auth Q]
18Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
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UniProt GroupP00698
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCR 21.3 alpha chainD [auth C],
I [auth G]
229Mus musculusMutation(s): 0 
Gene Names: H2-Ab1Tcra
UniProt
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UniProt GroupP01849
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
TCR 21.3 beta chainE [auth D],
J [auth H]
259Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for P01852 (Mus musculus)
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UniProt GroupP01852
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Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth I],
L [auth J]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
N [auth E]
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: 2.89 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.468α = 90
b = 99.391β = 90
c = 404.677γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
XPREPdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-04-10
    Changes: Structure summary
  • Version 1.3: 2013-05-15
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2018-01-24
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary