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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORITICAL MODEL OF TROPONIN
 
Authors :  K. Yadugiri, S. C. Mallena, K. M. Beesetti
Date :  19 Apr 02  (Deposition) - 01 May 02  (Release) - 20 Nov 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Theoritical Model Of Troponin, Muscle Protein, Calcium- Binding, Repeat, Acetylation, 3D-Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yadugiri, S. C. Mallena, K. M. Beesetti
Theoritical Model Of Troponin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TROPONIN C
    Chains: A
    Organism Common: PIG
    Organism Scientific: SUS SCROFA

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1LJ6)

(-) Sites  (0, 0)

(no "Site" information available for 1LJ6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LJ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Theoretical Model (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019776L29QTNNC1_HUMANDisease (CMH13)267607123AL21Q
2UniProtVAR_063071C84YTNNC1_HUMANDisease (CMH13)267607126AC76Y
3UniProtVAR_063072E134DTNNC1_HUMANDisease (CMH13)397516847AE126D
4UniProtVAR_063073D145ETNNC1_HUMANDisease (CMH13)267607124AD137E
5UniProtVAR_043988G159RTNNC1_HUMANDisease (CMD1Z)  ---AG151R
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 7)

Theoretical Model (2, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.TNNC1_PIG33-51
52-87
92-127
128-161		  4A:25-43
A:44-79
A:84-119
A:120-153
TNNC1_BOVIN33-51
52-87
92-127
128-161		  4A:25-43
A:44-79
A:84-119
A:120-153
TNNC1_HUMAN33-51
52-87
92-127
128-161		  4A:25-43
A:44-79
A:84-119
A:120-153
2EF_HAND_1PS00018 EF-hand calcium-binding domain.TNNC1_PIG65-77
105-117
141-153		  3A:57-69
A:97-109
A:133-145
TNNC1_BOVIN65-77
105-117
141-153		  3A:57-69
A:97-109
A:133-145
TNNC1_HUMAN65-77
105-117
141-153		  3A:57-69
A:97-109
A:133-145

(-) Exons   (0, 0)

(no "Exon" information available for 1LJ6)

(-) Sequences/Alignments

Theoretical Model
   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:153
 aligned with TNNC1_BOVIN | P63315 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   
          TNNC1_BOVIN     9 VEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLEELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE 161
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------Q------------------------------------------------------Y-------------------------------------------------D----------E-------------R-- SAPs(SNPs)
                PROSITE (1) ------------------------EF_HAND_2          EF_HAND_2  PDB: A:44-79             ----EF_HAND_2  PDB: A:84-119            EF_HAND_2  PDB: A:120-153          PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------------------------------------EF_HAND_1    ---------------------------EF_HAND_1    -----------------------EF_HAND_1    -------- PROSITE (6)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lj6 A   1 VEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLEELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain A from PDB  Type:PROTEIN  Length:153
 aligned with TNNC1_HUMAN | P63316 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   
          TNNC1_HUMAN     9 VEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLDELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE 161
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------Q------------------------------------------------------Y-------------------------------------------------D----------E-------------R-- SAPs(SNPs)
                PROSITE (2) ------------------------EF_HAND_2          EF_HAND_2  PDB: A:44-79             ----EF_HAND_2  PDB: A:84-119            EF_HAND_2  PDB: A:120-153          PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------EF_HAND_1    ---------------------------EF_HAND_1    -----------------------EF_HAND_1    -------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lj6 A   1 VEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLEELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain A from PDB  Type:PROTEIN  Length:153
 aligned with TNNC1_PIG | P63317 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   
            TNNC1_PIG     9 VEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLEELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE 161
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------Q------------------------------------------------------Y-------------------------------------------------D----------E-------------R-- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------EF_HAND_2          EF_HAND_2  PDB: A:44-79             ----EF_HAND_2  PDB: A:84-119            EF_HAND_2  PDB: A:120-153          PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------EF_HAND_1    ---------------------------EF_HAND_1    -----------------------EF_HAND_1    -------- PROSITE (5)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lj6 A   1 VEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDSKGKSEEELSDLFRMFDKNADGYIDLEELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (0, 0)

(no "SCOP Domain" information available for 1LJ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1LJ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LJ6)

(-) Gene Ontology  (23, 57)

Theoretical Model(hide GO term definitions)
Chain A   (TNNC1_PIG | P63317)
molecular function
    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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031013    troponin I binding    Interacting selectively and non-covalently with troponin I, the inhibitory subunit of the troponin complex.
    GO:0031014    troponin T binding    Interacting selectively and non-covalently with troponin T, the tropomyosin-binding subunit of the troponin complex.
biological process
    GO:0060048    cardiac muscle contraction    Muscle contraction of cardiac muscle tissue.
    GO:0043462    regulation of ATPase activity    Any process that modulates the rate of ATP hydrolysis by an ATPase.
    GO:0006937    regulation of muscle contraction    Any process that modulates the frequency, rate or extent of muscle contraction.
    GO:0032972    regulation of muscle filament sliding speed    Any process that modulates the velocity of muscle filament sliding.
    GO:0014883    transition between fast and slow fiber    The process of conversion of fast-contracting muscle fibers to a slower character. This may involve slowing of contractile rate, slow myosin gene induction, increase in oxidative metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
    GO:0055010    ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005861    troponin complex    A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.

Chain A   (TNNC1_HUMAN | P63316)
molecular function
    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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031013    troponin I binding    Interacting selectively and non-covalently with troponin I, the inhibitory subunit of the troponin complex.
    GO:0031014    troponin T binding    Interacting selectively and non-covalently with troponin T, the tropomyosin-binding subunit of the troponin complex.
biological process
    GO:0060048    cardiac muscle contraction    Muscle contraction of cardiac muscle tissue.
    GO:0002086    diaphragm contraction    A process in which force is generated within involuntary skeletal muscle tissue, resulting in a change in muscle geometry. This process occurs in the diaphragm. 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. The diaphragm is a striated muscle that is necessary for the process of respiratory gaseous exchange.
    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:0043462    regulation of ATPase activity    Any process that modulates the rate of ATP hydrolysis by an ATPase.
    GO:0006937    regulation of muscle contraction    Any process that modulates the frequency, rate or extent of muscle contraction.
    GO:0032972    regulation of muscle filament sliding speed    Any process that modulates the velocity of muscle filament sliding.
    GO:0010038    response to metal ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
    GO:0014883    transition between fast and slow fiber    The process of conversion of fast-contracting muscle fibers to a slower character. This may involve slowing of contractile rate, slow myosin gene induction, increase in oxidative metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
    GO:0055010    ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0043292    contractile fiber    Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005861    troponin complex    A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.

Chain A   (TNNC1_BOVIN | P63315)
molecular function
    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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031013    troponin I binding    Interacting selectively and non-covalently with troponin I, the inhibitory subunit of the troponin complex.
    GO:0031014    troponin T binding    Interacting selectively and non-covalently with troponin T, the tropomyosin-binding subunit of the troponin complex.
biological process
    GO:0060048    cardiac muscle contraction    Muscle contraction of cardiac muscle tissue.
    GO:0043462    regulation of ATPase activity    Any process that modulates the rate of ATP hydrolysis by an ATPase.
    GO:0006937    regulation of muscle contraction    Any process that modulates the frequency, rate or extent of muscle contraction.
    GO:0032972    regulation of muscle filament sliding speed    Any process that modulates the velocity of muscle filament sliding.
    GO:0014883    transition between fast and slow fiber    The process of conversion of fast-contracting muscle fibers to a slower character. This may involve slowing of contractile rate, slow myosin gene induction, increase in oxidative metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
    GO:0055010    ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005861    troponin complex    A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNNC1_HUMAN | P63316: 1ap4 1ih0 1j1d 1j1e 1lxf 1mxl 1ozs 1spy 1wrk 1wrl 2jt0 2jt3 2jt8 2jtz 2jxl 2kdh 2kfx 2kgb 2krd 2l1r 2l98 2mkp 2mle 2mlf 2mzp 2n79 2n7l 3rv5 3sd6 3swb 4gje 4gjf 4gjg 4y99 5vln 5w88

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LJ6)