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(-) Description

Title :  A STRUCTURAL BASIS FOR SELECTION AND CROSS-SPECIES REACTIVITY OF THE SEMI-INVARIANT NKT CELL RECEPTOR IN CD1D/GLYCOLIPID RECOGNITION
 
Authors :  L. Kjer-Nielsen, N. A. Borg
Date :  09 Nov 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Natural Killer T Cell Receptor, Nkt Cell Receptor, Nkt15, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kjer-Nielsen, N. A. Borg, D. G. Pellicci, T. Beddoe, L. Kostenko, C. S. Clements, N. A. Williamson, M. J. Smyth, G. S. Besra, H. H. Reid, M. Bharadwaj, D. I. Godfrey, J. Rossjohn, J. Mccluskey
A Structural Basis For Selection And Cross-Species Reactivity Of The Semi-Invariant Nkt Cell Receptor In Cd1D/Glycolipid Recognition
J. Exp. Med. V. 203 661 2006
PubMed-ID: 16505140  |  Reference-DOI: 10.1084/JEM.20051777
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NKT15
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - NKT15
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2EYT)

(-) Sites  (0, 0)

(no "Site" information available for 2EYT)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:22 -A:90
2A:139 -A:189
3A:164 -B:174
4B:23 -B:92
5B:148 -B:213
6C:22 -C:90
7C:139 -C:189
8C:164 -D:174
9D:23 -D:92
10D:148 -D:213

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:6 -Pro A:7
2Ser A:27 -Pro A:28
3Thr B:7 -Pro B:8
4Tyr B:154 -Pro B:155
5Ser C:6 -Pro C:7
6Ser C:27 -Pro C:28
7Thr D:7 -Pro D:8
8Tyr D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EYT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EYT)

(-) Exons   (0, 0)

(no "Exon" information available for 2EYT)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:202
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:202
                                                                                                                                            1                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88  
            TCA_HUMAN     - ----------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP  90
               SCOP domains d2eyta1 A:1-117 automated matches                                                                                 d2eyta2 A:118-205 automated matches                                                      SCOP domains
               CATH domains 2eytA01 A:1-116 Immunoglobulins                                                                                  ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeeee........eeeee.........eeeee................ee...eeeeehhhheeeeeeeee........................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eyt A   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP 205
                                    10        20        30        40        50        60|       71        81        91       103       113       123       133       143       153       163       173       183       193       203  
                                                                                      60|                                   100|                                                                                                      
                                                                                       62                                    103                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with TRBC2_HUMAN | A0A5B9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:243
                                                                                                                                              1                                                                                                                                
                                     -         -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126   
          TRBC2_HUMAN     - ------------------------------------------------------------------------------------------------------------------DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 129
               SCOP domains d2eytb1 B:3-119 automated matches                                                                                  d2eytb2 B:120-247 automated matches                                                                                              SCOP domains
               CATH domains 2eytB01 B:3-118 Immunoglobulins                                                                                   2eytB02 B:119-244 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee......eee.........eee...hhhhheeeeeeeeeeee..eeeeee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eyt B   3 DIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    12        22        32        42        52        62||      73        83        93       103|      114       124       134       144       154       164       174       184       194       204       214       224       234       244   
                                                                                       63|                                   103|                                                                                                                                              
                                                                                        65                                    105                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:202
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:202
                                                                                                                                            1                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88  
            TCA_HUMAN     - ----------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP  90
               SCOP domains d2eytc1 C:1-117 automated matches                                                                                 d2eytc2 C:118-205 automated matches                                                      SCOP domains
               CATH domains 2eytC01 C:1-116 Immunoglobulins                                                                                  ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeeehhh.eeeeee...hhhhheeeeeeee........eee...eeeeee........eeee.........eeeeee...............eee...eeeee....eeeeeeeeee.....hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eyt C   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP 205
                                    10        20        30        40        50        60|       71        81        91       103       113       123       133       143       153       163       173       183       193       203  
                                                                                      60|                                   100|                                                                                                      
                                                                                       62                                    103                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:243
 aligned with TRBC2_HUMAN | A0A5B9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:243
                                                                                                                                              1                                                                                                                                
                                     -         -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126   
          TRBC2_HUMAN     - ------------------------------------------------------------------------------------------------------------------DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 129
               SCOP domains d2eytd1 D:3-119 automated matches                                                                                  d2eytd2 D:120-247 automated matches                                                                                              SCOP domains
               CATH domains 2eytD01 D:3-118 Immunoglobulins                                                                                   2eytD02 D:119-244 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeee......ee......eee.........eee...hhhhheeeeeeeeeeee..eeeeee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eyt D   3 DIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    12        22        32        42        52        62||      73        83        93       103|      114       124       134       144       154       164       174       184       194       204       214       224       234       244   
                                                                                       63|                                   103|                                                                                                                                              
                                                                                        65                                    105
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a2eytA01A:1-116
1b2eytC01C:1-116
1c2eytB01B:3-118
1d2eytD01D:3-118
1e2eytB02B:119-244
1f2eytD02D:119-244

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EYT)

(-) Gene Ontology  (6, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (TCA_HUMAN | P01848)
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B,D   (TRBC2_HUMAN | A0A5B9)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  2eyt
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TCA_HUMAN | P01848: 1ao7 1bd2 1fyt 1j8h 1kgc 1mi5 1oga 1qrn 1qsf 1ymm 1zgl 2ak4 2bnq 2bnr 2bnu 2cdf 2cdg 2esv 2eyr 2eys 2f53 2f54 2gj6 2ial 2iam 2ian 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3dx9 3dxa 3ffc 3gsn 3he7 3hg1 3kpr 3kps 3kxf 3o4l 3o6f 3o8x 3o9w 3pwp 3qdg 3qdj 3qdm 3qeq 3qeu 3qib 3qjf 3qux 3scm 3sda 3sdc 3sdd 3sdx 3sjv 3skn 3t0e 3tn0 3tvm 4apq 4c56 4g8e 4g8f 4irs 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4prh 4pri 4prp 4udt 4udu 4ww1 4ww2 4wwk 4x6b 4x6c 4x6d 4y16 4y2d 4y4f 4y4h 4y4k 4zdh 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksa 5ksb
        TRBC2_HUMAN | A0A5B9: 1ao7 1bd2 2eyr 2eys 3kxf 3o6f 3o8x 3o9w 3qux 3t0e 3ta3 3tvm 4c56 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4udt 4udu 4ww1 4ww2 4wwk 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksa 5ksb

(-) Related Entries Specified in the PDB File

2eyr THE SEMI-INVARIANT NKT CELL RECEPTOR IN CD1D/GLYCOLIPID RECOGNITION
2eys THE SEMI-INVARIANT NKT CELL RECEPTOR IN CD1D/GLYCOLIPID RECOGNITION