Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SKELETAL MUSCLE TROPONIN IN THE CA2+-FREE STATE
 
Authors :  M. V. Vinogradova, D. B. Stone, G. G. Malanina, C. Karatzaferi, R. Cooke, R. A. Mendelson, R. J. Fletterick
Date :  14 Feb 05  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  7.00
Chains :  Asym. Unit :  C,I,T
Biol. Unit 1:  C,I,T  (1x)
Biol. Unit 2:  C,I,T  (2x)
Keywords :  Troponin, Off State, Thin Filament, Actin Binding, Muscle, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. V. Vinogradova, D. B. Stone, G. G. Malanina, C. Karatzaferi, R. Cooke, R. A. Mendelson, R. J. Fletterick
Ca2+-Regulated Structural Changes In Troponin
Proc. Natl. Acad. Sci. Usa V. 102 5038 2005
PubMed-ID: 15784741  |  Reference-DOI: 10.1073/PNAS.0408882102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TROPONIN T, FAST SKELETAL MUSCLE ISOFORMS
    ChainsT
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymTROPONIN T2
 
Molecule 2 - TROPONIN I, FAST SKELETAL MUSCLE
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymTROPONIN I, FAST-TWITCH ISOFORM
 
Molecule 3 - TROPONIN C, SKELETAL MUSCLE
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTNNC2
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit CIT
Biological Unit 1 (1x)CIT
Biological Unit 2 (2x)CIT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:107 , ASP C:109 , ASP C:113BINDING SITE FOR RESIDUE MG C 162
2AC2SOFTWAREASN C:143 , ASP C:145 , ASP C:149 , GLU C:152BINDING SITE FOR RESIDUE MG C 163

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YV0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YV0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YV0)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.TNNC2_CHICK18-53
54-89
94-129
130-163
  4C:16-52
C:53-85
C:96-127
C:128-161
2EF_HAND_1PS00018 EF-hand calcium-binding domain.TNNC2_CHICK31-43
67-79
107-119
143-155
  4C:29-42
C:66-78
C:105-117
C:141-153
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.TNNC2_CHICK18-53
54-89
94-129
130-163
  4C:16-52
C:53-85
C:96-127
C:128-161
2EF_HAND_1PS00018 EF-hand calcium-binding domain.TNNC2_CHICK31-43
67-79
107-119
143-155
  4C:29-42
C:66-78
C:105-117
C:141-153
Biological Unit 2 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.TNNC2_CHICK18-53
54-89
94-129
130-163
  8C:16-52
C:53-85
C:96-127
C:128-161
2EF_HAND_1PS00018 EF-hand calcium-binding domain.TNNC2_CHICK31-43
67-79
107-119
143-155
  8C:29-42
C:66-78
C:105-117
C:141-153

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSGALT000000110601ENSGALE00000073521Un_random:20732110-20732258149TNNC2_CHICK1-50501C:3-49 (gaps)47
1.2ENSGALT000000110602ENSGALE00000073519Un_random:20732332-20732446115TNNC2_CHICK50-88391C:49-8537
1.3ENSGALT000000110603ENSGALE00000073522Un_random:20732522-20732658137TNNC2_CHICK88-134471C:96-13237
1.4ENSGALT000000110604ENSGALE00000073520Un_random:20732749-20732979231TNNC2_CHICK134-143101C:132-14110

(-) 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 C from PDB  Type:PROTEIN  Length:148
 aligned with TNNC2_CHICK | P02588 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:159
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154         
          TNNC2_CHICK     5 TDQQAEARAFLSEEMIAEFKAAFDMFDADGGGDISTKELGTVMRMLGQNPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELANCFRIFDKNADGFIDIEELGEILRATGEHVTEEDIEDLMKDSDKNNDGRIDFDEFLKMMEGVQ 163
               SCOP domains d1yv0c1 C:3-161 Troponin C                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------EF_hand_5-1yv0C01 C:13-82                                            ---           ------------------------------------efhand-1yv0C03 C:132-160     - Pfam domains (1)
           Pfam domains (2) -----------------------------EF_hand_6-1yv0C02 C:32-85                                       ------------------------------------efhand-1yv0C04 C:132-160     - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh....................hhhhh........hhhhhh.....................-----------...hhhhhhhh......hhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------EF_HAND_2  PDB: C:16-52             EF_HAND_2  PDB: C:53-85             ----EF_HAND_2  PDB: C:96-127            EF_HAND_2  PDB: C:128-161          PROSITE (1)
                PROSITE (2) --------------------------EF_HAND_1    -----------------------EF_HAND_1    ---------------------------EF_HAND_1    -----------------------EF_HAND_1    -------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: C:3-49 (gaps) UniProt: 1-50    -------------------------------------Exon 1.3  PDB: C:96-132 UniProt: 88-134        ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.2  PDB: C:49-85 UniProt: 50-88  ---------------------------------------------Exon 1.4  -------------------- Transcript 1 (2)
                 1yv0 C   3 TDQQAEARAFLSEEMIAEFKAAFDMFDADGGGDISTKELGTVMRMLGQNPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQ-----------ELANCFRIFDKNADGFIDIEELGEILRATGEHVTEEDIEDLMKDSDKNNDGRIDFDEFLKMMEGVQ 161
                                    12        22        32   ||   43        53        63        73        83 |       -   |   102       112       122       132       142       152         
                                                            36|                                             85          96                                                                 
                                                             38                                                                                                                            

Chain I from PDB  Type:PROTEIN  Length:116
 aligned with TNNI2_CHICK | P68246 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:116
                                    13        23        33        43        53        63        73        83        93       103       113      
          TNNI2_CHICK     4 EEKKRRAATARRQHLKSAMLQLAVTEIEKEAAAKEVEKQNYLAEHCPPLSLPGSMQELQELCKKLHAKIDSVDEERYDTEVKLQKTNKELEDLSQKLFDLRGKFKRPPLRRVRMSA 119
               SCOP domains d1yv0i1 I:3-118 Troponin I                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Troponin-1yv0I01 I:14-118                                                                                 Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1yv0 I   3 EEKKRRAATARRQHLKSAMLQLAVTEIEKEAAAKEVEKQNYLAEHSPPLSLPGSMQELQELSKKLHAKIDSVDEERYDTEVKLQKTNKELEDLSQKLFDLRGKFKRPPLRRVRMSA 118
                                    12        22        32        42        52        62        72        82        92       102       112      

Chain T from PDB  Type:PROTEIN  Length:85
 aligned with TNNT3_CHICK | P12620 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:85
                                   174       184       194       204       214       224       234       244     
          TNNT3_CHICK   165 LAKADQKRGKKQTARETKKKVLAERRKPLNIDHLNEDKLRDKAKELWDWLYQLQTEKYDFAEQIKRKKYEIVTLRNRIDQAQKHS 249
               SCOP domains d1yv0t1 T:164-248 Troponin T                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains Troponin-1yv0T01 T:164-210                     -------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1yv0 T 164 LAKADQKRGKKQTARETKKKVLAERRKPLNIDHLNEDKLRDKAKELWDWLYQLQTEKYDFAEQIKRKKYEIVTLRNRIDQAQKHS 248
                                   173       183       193       203       213       223       233       243     

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YV0)

(-) Pfam Domains  (4, 6)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (11, 16)

Asymmetric Unit(hide GO term definitions)
Chain C   (TNNC2_CHICK | P02588)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0003009    skeletal muscle contraction    A process in which force is generated within skeletal 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. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
cellular component
    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 I   (TNNI2_CHICK | P68246)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0003009    skeletal muscle contraction    A process in which force is generated within skeletal 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. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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 T   (TNNT3_CHICK | P12620)
biological process
    GO:0006937    regulation of muscle contraction    Any process that modulates the frequency, rate or extent of muscle contraction.
    GO:0006942    regulation of striated muscle contraction    Any process that modulates the frequency, rate or extent of striated muscle contraction.
cellular component
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yv0)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yv0
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TNNC2_CHICK | P02588
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TNNI2_CHICK | P68246
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TNNT3_CHICK | P12620
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TNNC2_CHICK | P02588
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TNNI2_CHICK | P68246
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TNNT3_CHICK | P12620
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TNNC2_CHICK | P025881avs 1blq 1cta 1ctd 1ew7 1jc2 1ncx 1ncy 1ncz 1npq 1pon 1skt 1smg 1tnp 1tnq 1tnw 1tnx 1top 1ytz 1zac 2w49 2w4u 4tnc
        TNNI2_CHICK | P682461vdi 1vdj 1ytz 2w49 2w4u
        TNNT3_CHICK | P126201ytz 2w49 2w4u 2z5h

(-) Related Entries Specified in the PDB File

1ytz CRYSTAL STRUCTURE OF SKELETAL MUSCLE TROPONIN IN THE CA2+- ACTIVATED STATE