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(-) Description

Title :  STRUCTURE OF THE AB18.1 TCR
 
Authors :  A. M. Luoma, E. J. Adams
Date :  27 Oct 13  (Deposition) - 18 Dec 13  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin, Histocompatibility Antigens, T Cell Receptor, Immunological, Lymphocytes, T Cell Recognition, Activation, Gamma Delta T Cell, Human, Intraepithelial Lymphocytes, Cd1D, Glycolipids, Non-Classical Mhc, Glycoproteins, Cell-Surface Receptors, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Luoma, C. D. Castro, T. Mayassi, L. A. Bembinster, L. Bai, D. Picard, B. Anderson, L. Scharf, J. E. Kung, L. V. Sibener, P. B. Savage, B. Jabri, A. Bendelac, E. J. Adams
Crystal Structure Of V Delta 1 T Cell Receptor In Complex With Cd1D-Sulfatide Shows Mhc-Like Recognition Of A Self-Lipid By Human Gamma Delta T Cells.
Immunity V. 39 1032 2013
PubMed-ID: 24239091  |  Reference-DOI: 10.1016/J.IMMUNI.2013.11.001

(-) Compounds

Molecule 1 - T-CELL GAMMA PROTEIN,T-CELL RECEPTOR BETA-2 CHAIN C REGION
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: AB18.1 TCR GAMMA CHAIN
    Gene: TRBC2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HUMAN NKT TCR ALPHA CHAIN
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: AB18.1 TCR DELTA CHAIN
    Gene: B2M, HDCMA22P
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HUMAN NKT TCR BETA CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NDM)

(-) Sites  (0, 0)

(no "Site" information available for 4NDM)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:24 -A:96
2A:147 -A:212
3A:173 -B:168
4B:23 -B:91
5B:143 -B:193

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:153 -Pro A:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NDM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NDM)

(-) Exons   (0, 0)

(no "Exon" information available for 4NDM)

(-) Sequences/Alignments

Asymmetric/Biological 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains d4ndma1 A:9-118 automated matches                                                                             d4ndma2 A:119-246 automated matches                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee........eeeeeee......eeeeeee....eeee........eeee......eeeee...hhhhheeeeeeee.....eeeeeeeeeeee.hhhhh...eeeeee.hhhhhhhh.eeeeeeeeeee....eeeeeee..ee....eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ndm A   9 TKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYCATWDRNNKKLFGSGTTLVVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 246
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238        


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains d4ndmb1 B:1-121 automated matches                                                                                        d4ndmb2 B:122-212 automated matches                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eeee....eeeeeeee......eeeeeee.....eeeeeeee......ee..eeeeee....eeeeee...hhhhheeeeeeeee...........eeee...eeeeee........eeeeeee...eeeee...............eee...eeeee....eeeeeeeeee.......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ndm B   1 AQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGDQILYWGLSHTDKLIFGKGTRVTVEPNIQNPDPAVYQLRDSKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPE 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||144       154       164       174       184       194       204        
                                                                                                                                                                 136|                                                                       
                                                                                                                                                                  141
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  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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NDM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NDM)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NDM)

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  Cis Peptide Bonds
    Tyr A:153 - Pro A:154   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        K7N5M3_HUMAN | K7N5M3: 5e6i 5men
        K7N5M4_HUMAN | K7N5M4: 5brz 5bs0 5men
UniProtKB/TrEMBL
        K7N5M3_HUMAN | K7N5M3: 4en3 4mji 4mnh 4zak
        K7N5M4_HUMAN | K7N5M4: 4en3 4mnh
        Q6PJ56_HUMAN | Q6PJ56: 4lfh 4lhu 4mng 4mnh

(-) Related Entries Specified in the PDB File

4mng 4mnh 4mq7