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(-) Description

Title :  THE STRUCTURAL DYNAMICS AND ENERGETICS OF AN IMMUNODOMINANT T-CELL RECEPTOR ARE PROGRAMMED BY ITS VBETA DOMAIN
 
Authors :  J. Ishizuka, G. Stewart-Jones, A. Van Der Merwe, J. Bell, A. Mcmichae Y. Jones
Date :  15 Jan 08  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  D,E
Keywords :  Immune System, Host-Virus Interaction, Immune System/Receptor/Complex, Immunodominance, Immunoglobulin Domain, Tcr, Mhc, Flu, Mhc I, T-Cell, Complex, Membrane, Receptor, Immune Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ishizuka, G. Stewart-Jones, A. Van Der Merwe, J. Bell, A. Mcmichael, Y. Jones
The Structural Dynamics And Energetics Of An Immunodominant T-Cell Receptor Are Programmed By Its Vbeta Domain
Immunity V. 28 171 2008
PubMed-ID: 18275829  |  Reference-DOI: 10.1016/J.IMMUNI.2007.12.018

(-) Compounds

Molecule 1 - JM22 TCR ALPHA CHAIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - JM22 TCR BETA CHAIN
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : DE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2VLM)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1D:24 -D:90
2D:134 -D:184
3E:25 -E:93
4E:145 -E:210

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser D:8 -Pro D:9
2Ser E:9 -Pro E:10
3Tyr E:151 -Pro E:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VLM)

(-) 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 D from PDB  Type:PROTEIN  Length:184
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:199
                                                                                                                                        1                                                                                          
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82         
            TCA_HUMAN     - ------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS  91
               SCOP domains d2vlmd1 D:3-112 automated matches                                                                             d2vlmd2 D:113-201 automated match   es                                                    SCOP domains
               CATH domains 2vlmD01 D:3-111 Immunoglobulins                                                                              ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeee.....eeee..eeeee.....eeeeee...hhhhheeeeeeee......ee...eeeeee........eeeeeee......eeeeee........---.....eee.------------..eeeee......hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vlm D   3 QLLEQSPQFLSIQEGENLTVYCNSSSVFSSLQWYRQEPGEGPVLLVTVVTGGEVKKLKRLTFQFGDARKDSSLHITAAQPGDTGLYLCAGAGSQGNLIFGKGTKLSVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNV---KDSDVYITD------------SNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142  |   |152    |    -       172       182       192         
                                                                                                                                                                        145 149     157          170                               


Chain E from PDB  Type:PROTEIN  Length:240
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:240
                                                                                                                                          1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130
          TRBC1_HUMAN     - --------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains d2vlme1 E:5-115 automated matches                                                                              d2vlme2 E:116-244 automated matches                                                                                               SCOP domains
               CATH domains 2vlmE01 E:5-115 Immunoglobulins                                                                                2vlmE02 E:116-244 Immunoglobulins                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eee.........eee........eeeeeeee.......ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vlm E   5 GITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSSRSSYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 244
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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, 4)

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

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D   (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 E   (TRBC1_HUMAN | P01850)
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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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.

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  Cis Peptide Bonds
    Ser D:8 - Pro D:9   [ RasMol ]  
    Ser E:9 - Pro E:10   [ RasMol ]  
    Tyr E:151 - Pro E:152   [ RasMol ]  
 

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  2vlm
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  TRBC1_HUMAN | P01850
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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 2eyt 2f53 2f54 2gj6 2ial 2iam 2ian 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 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
        TRBC1_HUMAN | P01850: 1ao7 1fyt 1j8h 1kgc 1ktk 1mi5 1oga 1ymm 1zgl 2ak4 2axh 2bnq 2bnr 2bnu 2cde 2cdf 2cdg 2esv 2f53 2f54 2gj6 2ial 2iam 2ian 2nts 2nw2 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3d3v 3dx9 3dxa 3ffc 3he6 3hg1 3kpr 3kps 3o4l 3tn0 4g8e 4g8f 4gg6 4gg8 4iiq 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4l4t 4l4v 4l9l 4lcc 4lcw 4mji 4mnq 4nqc 4nqd 4nqe 4ozf 4ozg 4ozh 4ozi 4p46 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh

(-) Related Entries Specified in the PDB File

2vlj THE STRUCTURAL DYNAMICS AND ENERGETICS OF AN IMMUNODOMINANT T-CELL RECEPTOR ARE PROGRAMMED BY ITS VBETA DOMAIN
2vlk THE STRUCTURAL DYNAMICS AND ENERGETICS OF AN IMMUNODOMINANT T-CELL RECEPTOR ARE PROGRAMMED BY ITS VBETA DOMAIN
2vlr THE STRUCTURAL DYNAMICS AND ENERGETICS OF AN IMMUNODOMINANT T-CELL RECEPTOR ARE PROGRAMMED BY ITS VBETA DOMAIN