spacer
spacer

PDBsum entry 3he7
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Immune system PDB id
3he7

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
281 a.a. *
97 a.a. *
197 a.a. *
240 a.a. *
Ligands
NAG-NAG
NAG ×2
AGH
Waters ×45
* Residue conservation analysis
PDB id:
3he7
Name: Immune system
Title: Crystal structure of mouse cd1d-alpha-galactosylceramide with mouse valpha14-vbeta7 nkt tcr
Structure: Antigen-presenting glycoprotein cd1d1. Chain: a. Fragment: extracellular domain. Engineered: yes. Beta-2-microglobulin. Chain: b. Engineered: yes. Valpha14(mouse variable domain, human constant domain). Chain: c.
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: cd1d1, cd1.1. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Gene: b2m. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.226     R-free:   0.271
Authors: O.Patel,J.Rossjohn
Key ref: D.G.Pellicci et al. (2009). Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors. Immunity, 31, 47-59. PubMed id: 19592275
Date:
08-May-09     Release date:   28-Jul-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11609  (CD1D1_MOUSE) -  Antigen-presenting glycoprotein CD1d1 from Mus musculus
Seq:
Struc: 		336 a.a.
281 a.a.*
Protein chain
Pfam   ArchSchema ?
P01887  (B2MG_MOUSE) -  Beta-2-microglobulin from Mus musculus
Seq:
Struc: 		119 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P01848  (TCA_HUMAN) -  T cell receptor alpha chain constant from Homo sapiens
Seq:
Struc: 		140 a.a.
197 a.a.*
Protein chain
No UniProt id for this chain
Struc: 240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 21 residue positions (black crosses)

 

 
Immunity 31:47-59 (2009)
PubMed id: 19592275  
 
 
Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors.
D.G.Pellicci, O.Patel, L.Kjer-Nielsen, S.S.Pang, L.C.Sullivan, K.Kyparissoudis, A.G.Brooks, H.H.Reid, S.Gras, I.S.Lucet, R.Koh, M.J.Smyth, T.Mallevaey, J.L.Matsuda, L.Gapin, J.McCluskey, D.I.Godfrey, J.Rossjohn.
 
  ABSTRACT  
 
The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR alpha chain is typically invariant, the beta chain expression is more diverse, where three V beta chains are commonly expressed in mice. We report the structures of V alpha 14-V beta 8.2 and V alpha 14-V beta 7 NKT TCRs in complex with CD1d-alpha-galactosylceramide (alpha-GalCer) and the 2.5 A structure of the human NKT TCR-CD1d-alpha-GalCer complex. Both V beta 8.2 and V beta 7 NKT TCRs and the human NKT TCR ligated CD1d-alpha-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V beta domains of the V beta 8.2 and V beta 7 NKT TCR-CD1d complexes resulted in altered TCR beta-CD1d-mediated contacts and modulated recognition mediated by the invariant alpha chain. Mutagenesis studies revealed the differing contributions of V beta 8.2 and V beta 7 residues within the CDR2 beta loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V beta usage in NKT cells.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23154222 J.Rossjohn, D.G.Pellicci, O.Patel, L.Gapin, and D.I.Godfrey (2012).
Recognition of CD1d-restricted antigens by natural killer T cells.
  Nat Rev Immunol, 12, 845-857.  
  21283109 D.Christiansen, H.A.Vaughan, J.Milland, J.Miland, N.Dodge, E.Mouhtouris, M.J.Smyth, D.I.Godfrey, and M.S.Sandrin (2011).
Antibody responses to glycolipid-borne carbohydrates require CD4+ T cells but not CD1 or NKT cells.
  Immunol Cell Biol, 89, 502-510.  
21435579 E.J.Adams, and J.López-Sagaseta (2011).
The immutable recognition of CD1d.
  Immunity, 34, 281-283.  
21376639 K.S.Wun, G.Cameron, O.Patel, S.S.Pang, D.G.Pellicci, L.C.Sullivan, S.Keshipeddy, M.H.Young, A.P.Uldrich, M.S.Thakur, S.K.Richardson, A.R.Howell, P.A.Illarionov, A.G.Brooks, G.S.Besra, J.McCluskey, L.Gapin, S.A.Porcelli, D.I.Godfrey, and J.Rossjohn (2011).
A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells.
  Immunity, 34, 327-339.
PDB codes: 3arb 3ard 3are 3arf 3arg
21552205 S.Aspeslagh, Y.Li, E.D.Yu, N.Pauwels, M.Trappeniers, E.Girardi, T.Decruy, K.Van Beneden, K.Venken, M.Drennan, L.Leybaert, J.Wang, R.W.Franck, S.Van Calenbergh, D.M.Zajonc, and D.Elewaut (2011).
Galactose-modified iNKT cell agonists stabilized by an induced fit of CD1d prevent tumour metastasis.
  EMBO J, 30, 2294-2305.
PDB codes: 3qux 3quy 3quz
  21301478 S.Gras, L.Kjer-Nielsen, Z.Chen, J.Rossjohn, and J.McCluskey (2011).
The structural bases of direct T-cell allorecognition: implications for T-cell-mediated transplant rejection.
  Immunol Cell Biol, 89, 388-395.  
21376640 T.Mallevaey, A.J.Clarke, J.P.Scott-Browne, M.H.Young, L.C.Roisman, D.G.Pellicci, O.Patel, J.P.Vivian, J.L.Matsuda, J.McCluskey, D.I.Godfrey, P.Marrack, J.Rossjohn, and L.Gapin (2011).
A molecular basis for NKT cell recognition of CD1d-self-antigen.
  Immunity, 34, 315-326.
PDB codes: 3au1 3qi9
19949076 B.A.Sullivan, N.A.Nagarajan, G.Wingender, J.Wang, I.Scott, M.Tsuji, R.W.Franck, S.A.Porcelli, D.M.Zajonc, and M.Kronenberg (2010).
Mechanisms for glycolipid antigen-driven cytokine polarization by Valpha14i NKT cells.
  J Immunol, 184, 141-153.
PDB code: 3g08
20644577 D.I.Godfrey, J.Rossjohn, and J.McCluskey (2010).
Fighting infection with your MAITs.
  Nat Immunol, 11, 693-695.  
20139988 D.I.Godfrey, S.Stankovic, and A.G.Baxter (2010).
Raising the NKT cell family.
  Nat Immunol, 11, 197-206.  
20411526 D.J.Baek, Y.S.Lee, C.Lim, D.Lee, T.Lee, J.Y.Lee, K.A.Lee, W.J.Cho, C.Y.Kang, and S.Kim (2010).
Rational design and evaluation of a branched-chain-containing glycolipid antigen that binds to CD1d.
  Chem Asian J, 5, 1560-1564.  
20585371 G.Matulis, J.P.Sanderson, N.M.Lissin, M.B.Asparuhova, G.R.Bommineni, D.Schümperli, R.R.Schmidt, P.M.Villiger, B.K.Jakobsen, and S.D.Gadola (2010).
Innate-like control of human iNKT cell autoreactivity via the hypervariable CDR3beta loop.
  PLoS Biol, 8, e1000402.  
21124993 J.J.Miles, A.M.Bulek, D.K.Cole, E.Gostick, A.J.Schauenburg, G.Dolton, V.Venturi, M.P.Davenport, M.P.Tan, S.R.Burrows, L.Wooldridge, D.A.Price, P.J.Rizkallah, and A.K.Sewell (2010).
Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection.
  PLoS Pathog, 6, e1001198.
PDB code: 3o4l
20080535 J.Wang, Y.Li, Y.Kinjo, T.T.Mac, D.Gibson, G.F.Painter, M.Kronenberg, and D.M.Zajonc (2010).
Lipid binding orientation within CD1d affects recognition of Borrelia burgorferi antigens by NKT cells.
  Proc Natl Acad Sci U S A, 107, 1535-1540.
PDB codes: 3ilp 3ilq
20224567 L.Gapin (2010).
iNKT cell autoreactivity: what is 'self' and how is it recognized?
  Nat Rev Immunol, 10, 272-277.  
20080041 M.Salio, J.D.Silk, and V.Cerundolo (2010).
Recent advances in processing and presentation of CD1 bound lipid antigens.
  Curr Opin Immunol, 22, 81-88.  
19858073 M.Taniguchi, T.Tashiro, N.Dashtsoodol, N.Hongo, and H.Watarai (2010).
The specialized iNKT cell system recognizes glycolipid antigens and bridges the innate and acquired immune systems with potential applications for cancer therapy.
  Int Immunol, 22, 1-6.  
20534460 P.Arrenberg, R.Halder, Y.Dai, I.Maricic, and V.Kumar (2010).
Oligoclonality and innate-like features in the TCR repertoire of type II NKT cells reactive to a beta-linked self-glycolipid.
  Proc Natl Acad Sci U S A, 107, 10984-10989.  
20969594 R.Das, D.B.Sant'Angelo, and K.E.Nichols (2010).
Transcriptional control of invariant NKT cell development.
  Immunol Rev, 238, 195-215.  
20921281 Y.Li, E.Girardi, J.Wang, E.D.Yu, G.F.Painter, M.Kronenberg, and D.M.Zajonc (2010).
The Vα14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.
  J Exp Med, 207, 2383-2393.
PDB codes: 3o8x 3o9w
  20948595 L.Teyton (2009).
Natural killer T cell recognition of lipid antigens.
  F1000 Biol Rep, 1, 0.  
19816402 W.C.Florence, C.Xia, L.E.Gordy, W.Chen, Y.Zhang, J.Scott-Browne, Y.Kinjo, K.O.Yu, S.Keshipeddy, D.G.Pellicci, O.Patel, L.Kjer-Nielsen, J.McCluskey, D.I.Godfrey, J.Rossjohn, S.K.Richardson, S.A.Porcelli, A.R.Howell, K.Hayakawa, L.Gapin, D.M.Zajonc, P.G.Wang, and S.Joyce (2009).
Adaptability of the semi-invariant natural killer T-cell receptor towards structurally diverse CD1d-restricted ligands.
  EMBO J, 28, 3579-3590.  
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 codes are shown on the right.

 

spacer
spacer