6MNO

6235 TCR bound to I-Ab Padi4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+Tregcell development.

Stadinski, B.D.Blevins, S.J.Spidale, N.A.Duke, B.R.Huseby, P.G.Stern, L.J.Huseby, E.S.

(2019) Nat Immunol 20: 1046-1058

  • DOI: 10.1038/s41590-019-0414-1
  • Primary Citation of Related Structures:  
    6MKR, 6MKD, 6MNO, 6MNG, 6MNN, 6MNM

  • PubMed Abstract: 
  • The neonatal thymus generates Foxp3 + regulatory T (tT reg ) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tT reg cell selection is unresolved ...

    The neonatal thymus generates Foxp3 + regulatory T (tT reg ) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tT reg cell selection is unresolved. Here we identify 17 self-peptides recognized by neonatal tT reg cells, and reveal ligand specificity patterns that include self-antigens presented in an age- and inflammation-dependent manner. Fate-mapping studies of neonatal peptidyl arginine deiminase type IV (Padi4)-specific thymocytes reveal disparate fate choices. Neonatal thymocytes expressing T cell receptors that engage IA b -Padi4 with moderate dwell times within a conventional docking orientation are exported as tT reg cells. In contrast, Padi4-specific T cell receptors with short dwell times are expressed on CD4 + T cells, while long dwell times induce negative selection. Temporally, Padi4-specific thymocytes are subject to a developmental stage-specific change in negative selection, which precludes tT reg cell development. Thus, a temporal switch in negative selection and ligand binding kinetics constrains the neonatal tT reg selection window.


    Organizational Affiliation

    Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA. Eric.Huseby@umassmed.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-B alpha chainA [auth C]179Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus)
Explore P14434 
Go to UniProtKB:  P14434
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Padi4 (92-105) peptide and MHC Class II I-Ab beta chainB [auth D]217Mus musculusMutation(s): 0 
Gene Names: Padi4Pad4Pdi4H2-Ab1H2-iabeta
EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Find proteins for Q9Z183 (Mus musculus)
Explore Q9Z183 
Go to UniProtKB:  Q9Z183
IMPC:  MGI:1338898
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
6235 TCR alpha chainC [auth A]208Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
6235 TCR beta chainD [auth B]239Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 250.057α = 90
b = 69.03β = 91.51
c = 64.687γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references