PDBsum entry 1kt2

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protein ligands Protein-protein interface(s) links
Immune system PDB id
Jmol PyMol
Protein chains
182 a.a. *
213 a.a. *
NAG ×4
Waters ×215
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of class ii mhc molecule iek bound to moth cytochromE C peptide
Structure: H-2 class ii histocompatibility antigen, e-d alph chain: a, c. Engineered: yes. Fusion protein consisting of cytochromE C peptide rich linker, and mhc e-beta-k. Chain: b, d. Engineered: yes. Other_details: fusion protein consists of moth cytochromE C residues 1-14 (adliaylkqatk), glycine rich linker, residues
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Lonomia obliqua, mus musculus. , House mouse. Organism_taxid: 304329,10090.
Biol. unit: Tetramer (from PQS)
2.80Å     R-factor:   0.220     R-free:   0.294
Authors: D.H.Fremont,S.Dai,H.Chiang,F.Crawford,P.Marrack,J.Kappler
Key ref: D.H.Fremont et al. (2002). Structural basis of cytochrome c presentation by IE(k). J Exp Med, 195, 1043-1052. PubMed id: 11956295
15-Jan-02     Release date:   01-May-02    
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Protein chains
Pfam   ArchSchema ?
P01904  (HA21_MOUSE) -  H-2 class II histocompatibility antigen, E-D alpha chain
255 a.a.
182 a.a.*
Protein chains
Pfam   ArchSchema ?
P04230  (HB21_MOUSE) -  H-2 class II histocompatibility antigen, E-B beta chain
264 a.a.
213 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 30 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     immune response   2 terms 


J Exp Med 195:1043-1052 (2002)
PubMed id: 11956295  
Structural basis of cytochrome c presentation by IE(k).
D.H.Fremont, S.Dai, H.Chiang, F.Crawford, P.Marrack, J.Kappler.
The COOH-terminal peptides of pigeon and moth cytochrome c, bound to mouse IE(k), are two of the most thoroughly studied T cell antigens. We have solved the crystal structures of the moth peptide and a weak agonist-antagonist variant of the pigeon peptide bound to IE(k). The moth peptide and all other peptides whose structures have been solved bound to IE(k), have a lysine filling the p9 pocket of IE(k). However, the pigeon peptide has an alanine at p9 shifting the lysine to p10. Rather than kinking to place the lysine in the anchor pocket, the pigeon peptide takes the extended course through the binding groove, which is characteristic of all other peptides bound to major histocompatibility complex (MHC) class II. Thus, unlike MHC class I, in which peptides often kink to place optimally anchoring side chains, MHC class II imposes an extended peptide conformation even at the cost of a highly conserved anchor residue. The substitution of Ser for Thr at p8 in the variant pigeon peptide induces no detectable surface change other than the loss of the side chain methyl group, despite the dramatic change in recognition by T cells. Finally, these structures can be used to interpret the many published mutational studies of these ligands and the T cell receptors that recognize them.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20007533 C.K.Baumgartner, A.Ferrante, M.Nagaoka, J.Gorski, and L.P.Malherbe (2010).
Peptide-MHC class II complex stability governs CD4 T cell clonal selection.
  J Immunol, 184, 573-581.  
20331477 C.K.Baumgartner, and L.P.Malherbe (2010).
Regulation of CD4 T-cell receptor diversity by vaccine adjuvants.
  Immunology, 130, 16-22.  
20462374 H.McConnell (2010).
Adventures in physical chemistry.
  Annu Rev Biophys, 39, 1.  
19801984 W.L.Lo, N.J.Felix, J.J.Walters, H.Rohrs, M.L.Gross, and P.M.Allen (2009).
An endogenous peptide positively selects and augments the activation and survival of peripheral CD4+ T cells.
  Nat Immunol, 10, 1155-1161.  
18779568 F.Menconi, M.C.Monti, D.A.Greenberg, T.Oashi, R.Osman, T.F.Davies, Y.Ban, E.M.Jacobson, E.S.Concepcion, C.W.Li, and Y.Tomer (2008).
Molecular amino acid signatures in the MHC class II peptide-binding pocket predispose to autoimmune thyroiditis in humans and in mice.
  Proc Natl Acad Sci U S A, 105, 14034-14039.  
18697946 S.Dai, F.Crawford, P.Marrack, and J.W.Kappler (2008).
The structure of HLA-DR52c: comparison to other HLA-DRB3 alleles.
  Proc Natl Acad Sci U S A, 105, 11893-11897.
PDB code: 3c5j
17703931 A.L.DeMond, and J.T.Groves (2007).
Interrogating the T cell synapse with patterned surfaces and photoactivated proteins.
  Curr Opin Immunol, 19, 722-727.  
17291278 Y.H.Chien, and Y.Konigshofer (2007).
Antigen recognition by gammadelta T cells.
  Immunol Rev, 215, 46-58.  
16537380 S.Qi, M.Krogsgaard, M.M.Davis, and A.K.Chakraborty (2006).
Molecular flexibility can influence the stimulatory ability of receptor-ligand interactions at cell-cell junctions.
  Proc Natl Acad Sci U S A, 103, 4416-4421.  
15213134 K.M.Williams, and E.C.Bigley (2004).
Identification of an I-Ed-restricted T-cell epitope of Escherichia coli outer membrane protein F.
  Infect Immun, 72, 3907-3913.  
15331779 Z.Zavala-Ruiz, I.Strug, B.D.Walker, P.J.Norris, and L.J.Stern (2004).
A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition.
  Proc Natl Acad Sci U S A, 101, 13279-13284.
PDB codes: 1sje 1sjh
15489166 Z.Zavala-Ruiz, I.Strug, M.W.Anderson, J.Gorski, and L.J.Stern (2004).
A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins.
  Chem Biol, 11, 1395-1402.
PDB codes: 1t5w 1t5x
12909456 D.Housset, and B.Malissen (2003).
What do TCR-pMHC crystal structures teach us about MHC restriction and alloreactivity?
  Trends Immunol, 24, 429-437.  
14690592 M.Krogsgaard, N.Prado, E.J.Adams, X.L.He, D.C.Chow, D.B.Wilson, K.C.Garcia, and M.M.Davis (2003).
Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation.
  Mol Cell, 12, 1367-1378.
PDB codes: 1r5v 1r5w
12152083 L.C.Wu, D.S.Tuot, D.S.Lyons, K.C.Garcia, and M.M.Davis (2002).
Two-step binding mechanism for T-cell receptor recognition of peptide MHC.
  Nature, 418, 552-556.  
12084926 X.Liu, S.Dai, F.Crawford, R.Fruge, P.Marrack, and J.Kappler (2002).
Alternate interactions define the binding of peptides to the MHC molecule IA(b).
  Proc Natl Acad Sci U S A, 99, 8820-8825.
PDB code: 1lnu
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.