6MNM

6256 TCR bound to I-Ab Padi4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-B alpha chainC180Mus musculusMutation(s): 0 
Gene Names: H2-Aa
Find proteins for P14434 (Mus musculus)
Explore P14434 
Go to UniProtKB:  P14434
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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 chainD217Mus musculusMutation(s): 0 
Gene Names: Padi4Pad4Pdi4
EC: 3.5.3.15
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Find proteins for Q9Z183 (Mus musculus)
Explore Q9Z183 
Go to UniProtKB:  Q9Z183
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
6256 TCR alpha chainA208Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
6256 TCR beta chainB239Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.351α = 90
b = 73.771β = 90.52
c = 63.142γ = 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 

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