6MKD

4699 TCR bound to I-Ab Padi4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report

Currently 6MKD does not have a validation slider image.


This is version 1.2 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: https://doi.org/10.1038/s41590-019-0414-1
  • Primary Citation of Related Structures:  
    6MKD, 6MKR, 6MNG, 6MNM, 6MNN, 6MNO

  • 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14434
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Z183P14483
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
4699 TCR alpha chainC [auth A]208Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
4699 TCR beta chainD [auth B]239Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 255.448α = 90
b = 73.643β = 90.39
c = 64.566γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Currently 6MKD does not have a validation slider image.



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
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description