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(-) Description

Title :  STRUCTURE OF TROPOMYOSIN'S MID-REGION: BENDING AND BINDING SITES FOR ACTIN
 
Authors :  J. H. Brown, Z. Zhou, L. Reshetnikova, H. Robinson, R. D. Yammani, L. S. Tobacman, C. Cohen
Date :  11 Oct 05  (Deposition) - 03 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Helix, Coiled Coil, Alanine, Axial Stagger, Radius, Side-Chain Packing, Crystal Packing, Temperature Factor, Cardiomyopathy, Elongated Protein, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Brown, Z. Zhou, L. Reshetnikova, H. Robinson, R. D. Yammani, L. S. Tobacman, C. Cohen
Structure Of The Mid-Region Of Tropomyosin: Bending And Binding Sites For Actin.
Proc. Natl. Acad. Sci. Usa V. 102 18878 2005
PubMed-ID: 16365313  |  Reference-DOI: 10.1073/PNAS.0509269102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STRIATED-MUSCLE ALPHA TROPOMYOSIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 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 2B9C)

(-) Sites  (0, 0)

(no "Site" information available for 2B9C)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:190 -B:1190

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B9C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B9C)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TROPOMYOSINPS00326 Tropomyosins signature.TPM1_RAT232-240
 
  2A:213-213
B:1213-1213

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000408081ENSRNOE00000390314chr8:71358063-71357844220TPM1_RAT1-38380--
1.2ENSRNOT000000408082ENSRNOE00000176519chr8:71357072-71356947126TPM1_RAT39-80420--
1.5ENSRNOT000000408085ENSRNOE00000289049chr8:71344964-71344831134TPM1_RAT81-125452A:98-125
B:1093-1125
28
33
1.6ENSRNOT000000408086ENSRNOE00000337985chr8:71342905-71342788118TPM1_RAT125-164402A:125-164
B:1125-1164
40
40
1.7ENSRNOT000000408087ENSRNOE00000229797chr8:71341716-7134164671TPM1_RAT165-188242A:165-188
B:1165-1188
24
24
1.8ENSRNOT000000408088ENSRNOE00000176098chr8:71341393-7134131876TPM1_RAT188-213262A:188-208
B:1188-1208
21
21
1.10ENSRNOT0000004080810ENSRNOE00000310303chr8:71340384-7134032263TPM1_RAT214-234212A:209-213
B:1209-1213
5
5
1.11ENSRNOT0000004080811ENSRNOE00000229785chr8:71340066-7133999770TPM1_RAT235-258242A:214-233
B:1214-1234
20
21
1.15ENSRNOT0000004080815ENSRNOE00000322655chr8:71332155-71331307849TPM1_RAT258-284270--

(-) 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:136
 aligned with TPM1_RAT | P04692 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:157
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       
            TPM1_RAT     98 ELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSID  254
               SCOP domains d2b9ca1 A:98-208 Tropomyosin                                                                                   ---------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------hh..hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------TROPOMYOS-------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:98-125     ---------------------------------------Exon 1.7  PDB: A:165-188-------------------------Exon 1.10            Exon 1.11            Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.6  PDB: A:125-164                -----------------------Exon 1.8  PDB: A:188-208  ----------------------------------------- Transcript 1 (2)
                2b9c A   98 ELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLE---------------------DKVEELLSKNYHLENEVARLKKLVG  233
                                   107       117       127       137       147       157       167       177       187       197       207|        -         -  |    216       226       
                                                                                                                                        208                   209                        

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with TPM1_RAT | P04692 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:163
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   
            TPM1_RAT     93 QLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDD  255
               SCOP domains -----d2b9cb1 B:1098-1208 Tropomyosin                                                                                ----------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------TROPOMYOS--------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:1093-1125       ---------------------------------------Exon 1.7                -------------------------Exon 1.10            Exon 1.11             Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.6  PDB: B:1125-1164              -----------------------Exon 1.8  PDB: B:1188-1208------------------------------------------ Transcript 1 (2)
                2b9c B 1093 QLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLE---------------------DKVEELLSKNYHLENEVARLKKLVGE 1234
                                  1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202     |   -         -      1211      1221      1231   
                                                                                                                                            1208                  1209                         

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B9C)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPM1_RAT | P04692)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0051693    actin filament capping    The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0060048    cardiac muscle contraction    Muscle contraction of cardiac muscle tissue.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0030049    muscle filament sliding    The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0051496    positive regulation of stress fiber assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
    GO:0043462    regulation of ATPase activity    Any process that modulates the rate of ATP hydrolysis by an ATPase.
    GO:0031529    ruffle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPM1_RAT | P046921ihq 1mv4 1tmz 2g9j 3azd

(-) Related Entries Specified in the PDB File

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