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(-) Description

Title :  STRUCTURE OF XV19 VALPHA1-VBETA16 TYPE-II NATURAL KILLER T CELL RECEPTOR
 
Authors :  O. Patel, J. Rossjohn
Date :  04 Apr 12  (Deposition) - 25 Jul 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Natural Killer T Cell Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Patel, D. G. Pellicci, S. Gras, M. L. Sandoval-Romero, A. P. Uldrich T. Mallevaey, A. J. Clarke, J. Le Nours, A. Theodossis, S. L. Cardell, L. Gapin, D. I. Godfrey, J. Rossjohn
Recognition Of Cd1D-Sulfatide Mediated By A Type Ii Natural Killer T Cell Antigen Receptor.
Nat. Immunol. V. 13 857 2012
PubMed-ID: 22820603  |  Reference-DOI: 10.1038/NI.2372

(-) Compounds

Molecule 1 - VALPHA1 XV19 TYPE II NATURAL KILLER T CELL RECEPTOR (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN (SEE REMARK 999)
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 2 - VBETA16 XV19 TYPE II NATURAL KILLER T CELL RECEPTOR (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN (SEE REMARK 999)
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4EI6)

(-) Sites  (0, 0)

(no "Site" information available for 4EI6)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:89
2A:136 -A:186
3A:161 -B:171
4B:23 -B:92
5B:145 -B:210
6C:23 -C:89
7C:136 -C:186
8C:161 -D:171
9D:23 -D:92
10D:145 -D:210

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Ile B:7 -Pro B:8
3Gln B:80 -Pro B:81
4Tyr B:151 -Pro B:152
5Ser C:7 -Pro C:8
6Ile D:7 -Pro D:8
7Gln D:80 -Pro D:81
8Tyr D:151 -Pro D:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EI6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EI6)

(-) Exons   (0, 0)

(no "Exon" information available for 4EI6)

(-) 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
                                                                                                                                                                                                                                          
               SCOP domains d4ei6a1 A:2-114 automated matches                                                                                d4ei6a2 A:115-203 automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee....eeeeeeeee......eeeee....eeeee..eeeeee....eeeeee...hhhhheeeeeeeee........ee...eeeeee........eeeeee.......eeeeee................ee...eeeeehhhheeeeeeeee......hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ei6 A   2 QKVQQSPESLSVPEGGMASLNCTSSDRNFQYFWWYRQHSGEGPKALMSIFSDGDKKEGRFTAHLNKASLHVSLHIRDSQPSDSALYFCAASEQNNYAQGLTFGLGTRVSVFPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4ei6b1 B:0-115 automated matches                                                                                   d4ei6b2 B:116-243 automated matches                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeee....eeeeee......eeeeeeee...eeeeeeeee..eeeee.......eeee......eeeee...hhhhheeeeeeee........ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ei6 B   0 MGPKVLQIPSHQIIDMGQMVTLNCDPVSNHLYFYWYKQILGQQMEFLVNFYNGKVMEKSKLFKDQFSVERPDGSYFTLKIQPTALEDSAVYFCASSFWGAYAEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 243
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    


Chain C from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains d4ei6c1 C:2-114 automated matches                                                                                d4ei6c2 C:115-202 automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee....eeeeeeeee......eeeeee...eeeee..eeeeeehhh.eeeeee...hhhhheeeeeeeee........ee...eeeeee......eeeee....eeeee.............eee...eeeeehhhheeeeeeeeee..hhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ei6 C   2 QKVQQSPESLSVPEGGMASLNCTSSDRNFQYFWWYRQHSGEGPKALMSIFSDGDKKEGRFTAHLNKASLHVSLHIRDSQPSDSALYFCAASEQNNYAQGLTFGLGTRVSVFPYIPDPAVYQLRDSSVCLFTDFDSQTNVSQSSDVYITDKCVLDMRSMDFKSNSAVAWSNFACANAFNNSIIPEDTFFP 202
                                    11        21        31        41        51        61        71        81        91       101       111   ||  123    || 138       148 ||    160       170       180|      193         
                                                                                                                                           115|       128|             150|                        180|                  
                                                                                                                                            118        134              153                         184                  


Chain D from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4ei6d1 D:3-115 automated matches                                                                                d4ei6d2 D:116-243 automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeee....eeeeee......eeeeeeee...eeeeeeeee..eeeee.......eeee......eeeee...hhhhheeeeeeee........ee...eeeeee.........eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ei6 D   3 KVLQIPSHQIIDMGQMVTLNCDPVSNHLYFYWYKQILGQQMEFLVNFYNGKVMEKSKLFKDQFSVERPDGSYFTLKIQPTALEDSAVYFCASSFWGAYAEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 243
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
   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  (0, 0)

(no "CATH Domain" information available for 4EI6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EI6)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4EI6)

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  Cis Peptide Bonds
    Gln B:80 - Pro B:81   [ RasMol ]  
    Gln D:80 - Pro D:81   [ RasMol ]  
    Ile B:7 - Pro B:8   [ RasMol ]  
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 Related Entries

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4ei5