6MKD

4699 TCR bound to I-Ab Padi4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 

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:  

  • PubMed Abstract: 
  • The neonatal thymus generates Foxp3 <sup>+ </sup> regulatory T (tT <sub>reg </sub>) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tT <sub>reg </sub> 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 Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA. Eric.Huseby@umassmed.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, A-B alpha chain
C
179Mus musculusMutation(s): 0 
Gene Names: H2-Aa
Find proteins for P14434 (Mus musculus)
Go to UniProtKB:  P14434
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain
D
217Mus musculusMutation(s): 0 
Gene Names: H2-Ab1 (H2-iabeta), Padi4 (Pad4, Pdi4)
EC: 3.5.3.15
Find proteins for P14483 (Mus musculus)
Go to UniProtKB:  P14483
Find proteins for Q9Z183 (Mus musculus)
Go to UniProtKB:  Q9Z183
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
4699 TCR alpha chain
A
208N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
4699 TCR beta chain
B
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 255.448α = 90.00
b = 73.643β = 90.39
c = 64.566γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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