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(-) Description

Title :  T36-5 TCR SPECIFIC FOR HLA-A24-NEF134-10
 
Authors :  A. Shimizu, S. Fukai, A. Yamagata, A. Iwamoto
Date :  20 Sep 12  (Deposition) - 23 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hiv-1, Nef, Immune System, T Cell Receptor, Immunogloburin Domain, Tcr, Immune Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shimizu, A. Kawana-Tachikawa, A. Yamagata, C. Han, D. Zhu, Y. Sato, H. Nakamura, T. Koibuchi, J. Carlson, E. Martin, C. J. Brumme, Y. Shi, G. F. Gao, Z. L. Brumme, S. Fukai, A. Iwamoto
Structure Of Tcr And Antigen Complexes At An Immunodominant Ctl Epitope In Hiv-1 Infection
Sci Rep V. 3 3097 2013
PubMed-ID: 24192765  |  Reference-DOI: 10.1038/SREP03097

(-) Compounds

Molecule 1 - T36-5 TCR ALPHA CHAIN
    Chains: C, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - T36-5 TCR BETA CHAIN
    Chains: D, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21
    Expression System Taxid: 562
    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):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VXT)

(-) Sites  (0, 0)

(no "Site" information available for 3VXT)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:133 -A:183
2A:158 -B:168
3B:23 -B:91
4B:142 -B:207
5C:133 -C:183
6C:158 -D:168
7D:23 -D:91
8D:142 -D:207

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn D:7 -Pro D:8
2Tyr D:148 -Pro D:149
3Asn B:7 -Pro B:8
4Tyr B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VXT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VXT)

(-) Exons   (0, 0)

(no "Exon" information available for 3VXT)

(-) 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:199
                                                                                                                                                                                                                                       
               SCOP domains d3vxta1 A:2-111 automated matches                                                                             d3vxta2 A:112-200 automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eeeeee........eeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhheeeeeeee.....eeeeeeeeeeee........eeeee........eeeeee................ee...eeeeehhhheeeeeeeeee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vxt A   2 KEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLWGTYNQGGKLIFGQGTELSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         


Chain B from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d3vxtb1 B:1-112 automated matches                                                                               d3vxtb2 B:113-241 automated matches                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eee.........eee...hhhhheeeeeeee.....eee...eeeeee.hhhhh...eeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vxt B   1 EAQVTQNPRYLITVTGKKLTVTCSQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGDVPEGYKVSRKEKRNFPLILESPSPNQTSLYFCASSGASHEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 


Chain C from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d3vxtc1 C:2-111 automated matches                                                                             d3vxtc2 C:112-200 automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eeeeee........eeeeee......eeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeee.....eeeeeeeeeeee........eeeee........eeeeee................eeeeeeeeeehhhheeeeeeeeee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vxt C   2 KEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLWGTYNQGGKLIFGQGTELSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         


Chain D from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d3vxtd1 D:1-112 automated matches                                                                               d3vxtd2 D:113-241 automated matches                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeeeee..eeee.......ee.........eee...hhhhheeeeeeee.....eee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vxt D   1 EAQVTQNPRYLITVTGKKLTVTCSQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGDVPEGYKVSRKEKRNFPLILESPSPNQTSLYFCASSGASHEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 3VXT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VXT)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3VXT)

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  Cis Peptide Bonds
    Asn B:7 - Pro B:8   [ RasMol ]  
    Asn D:7 - Pro D:8   [ RasMol ]  
    Tyr B:148 - Pro B:149   [ RasMol ]  
    Tyr D:148 - Pro D:149   [ RasMol ]  
 
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  3vxt
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 Related Entries

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(-) Related Entries Specified in the PDB File

3vxm 3vxn 3vxo 3vxp 3vxq 3vxr 3vxs 3vxu