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(-) Description

Title :  COILED-COIL DOMAIN OF DMPK
 
Authors :  P. Garcia, M. Marino, O. Mayans
Date :  16 Nov 04  (Deposition) - 16 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Coiled-Coil, Kinase Activation, Dmpk, Molecular Replacement, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Garcia, Z. Ucurum, R. Bucher, D. I. Svergun, T. Huber, A. Lustig, P. V. Konarev, M. Marino, O. Mayans
Molecular Insights Into The Self-Assembly Mechanism Of Dystrophia Myotonica Kinase
Faseb J. V. 20 1142 2006
PubMed-ID: 16770013  |  Reference-DOI: 10.1096/FJ.05-5262COM
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYOTONIN-PROTEIN KINASE
    ChainsA, B, D
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPETM-11
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentWILD-TYPE COILED-COIL DOMAIN OF DPMK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMYOTONIC DYSTROPHY PROTEIN KINASE, MDPK, DM-KINASE, DMK, DMPK, MT-PK

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WT6)

(-) Sites  (0, 0)

(no "Site" information available for 1WT6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WT6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WT6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WT6)

(-) Exons   (2, 6)

Asymmetric/Biological Unit (2, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002912701aENSE00001112734chr19:46285815-46285451365DMPK_HUMAN1-54540--
1.2cENST000002912702cENSE00001257024chr19:46283127-4628303692DMPK_HUMAN54-84310--
1.3ENST000002912703ENSE00001598066chr19:46282780-4628269784DMPK_HUMAN85-112280--
1.4ENST000002912704ENSE00001157031chr19:46282617-4628252296DMPK_HUMAN113-144320--
1.5ENST000002912705ENSE00001112730chr19:46281899-46281751149DMPK_HUMAN145-194500--
1.6ENST000002912706ENSE00001112733chr19:46281478-4628138594DMPK_HUMAN194-225320--
1.7ENST000002912707ENSE00001112727chr19:46281131-46280925207DMPK_HUMAN226-294690--
1.8bENST000002912708bENSE00001256892chr19:46280848-46280585264DMPK_HUMAN295-382880--
1.9ENST000002912709ENSE00001112731chr19:46278292-4627820786DMPK_HUMAN383-411290--
1.10ENST0000029127010ENSE00001112739chr19:46276010-46275899112DMPK_HUMAN411-448380--
1.11ENST0000029127011ENSE00001256867chr19:46275186-46275029158DMPK_HUMAN449-501533A:6-42
B:2-42
D:6-42
37
41
37
1.12ENST0000029127012ENSE00001112726chr19:46274923-4627482698DMPK_HUMAN501-534343A:42-70
B:42-68
D:42-68
29
27
27
1.13ENST0000029127013ENSE00001112736chr19:46274654-4627460847DMPK_HUMAN534-549160--
1.14bENST0000029127014bENSE00001707544chr19:46274318-4627422990DMPK_HUMAN550-579300--
1.15bENST0000029127015bENSE00001655086chr19:46273898-46272978921DMPK_HUMAN580-629500--

(-) 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:65
 aligned with DMPK_HUMAN | Q09013 from UniProtKB/Swiss-Prot  Length:629

    Alignment length:65
                                   474       484       494       504       514       524     
           DMPK_HUMAN   465 EVTLRELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELLQA 529
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains 1wt6A00 A:6-70  [code=1.20.5.340, no name defined]                CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: A:6-42 [INCOMPLETE]  ---------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.12  PDB: A:42-70       Transcript 1 (2)
                 1wt6 A   6 EVTLRELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELLQA  70
                                    15        25        35        45        55        65     

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with DMPK_HUMAN | Q09013 from UniProtKB/Swiss-Prot  Length:629

    Alignment length:67
                                   470       480       490       500       510       520       
           DMPK_HUMAN   461 EAEAEVTLRELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELL 527
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains 1wt6B00 B:2-68  [code=1.20.5.340, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: B:2-42 UniProt: 449-501  -------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.12  PDB: B:42-68     Transcript 1 (2)
                 1wt6 B   2 EAEAEVTLRELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELL  68
                                    11        21        31        41        51        61       

Chain D from PDB  Type:PROTEIN  Length:63
 aligned with DMPK_HUMAN | Q09013 from UniProtKB/Swiss-Prot  Length:629

    Alignment length:63
                                   474       484       494       504       514       524   
           DMPK_HUMAN   465 EVTLRELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELL 527
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains 1wt6D00 D:6-68  [code=1.20.5.340, no name defined]              CATH domains
           Pfam domains (1) ---------------DMPK_coil-1wt6D01 D:21-68                        Pfam domains (1)
           Pfam domains (2) ---------------DMPK_coil-1wt6D02 D:21-68                        Pfam domains (2)
           Pfam domains (3) ---------------DMPK_coil-1wt6D03 D:21-68                        Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: D:6-42 [INCOMPLETE]  -------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.12  PDB: D:42-68     Transcript 1 (2)
                 1wt6 D   6 EVTLRELQEALEEEVLTRQSLSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELL  68
                                    15        25        35        45        55        65   

   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 1WT6)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,D   (DMPK_HUMAN | Q09013)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017020    myosin phosphatase regulator activity    Modulation of the activity of the enzyme myosin phosphatase.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0010657    muscle cell apoptotic process    A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
    GO:0006998    nuclear envelope organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:1903779    regulation of cardiac conduction    Any process that modulates the frequency, rate or extent of cardiac conduction.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0014853    regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction    Any process, involved in skeletal muscle contraction, that modulates the establishment or extent of the excitatory postsynaptic potential (EPSP). Excitatory postsynaptic potential (EPSP) is a temporay increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0008016    regulation of heart contraction    Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
    GO:0010830    regulation of myotube differentiation    Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    GO:0014722    regulation of skeletal muscle contraction by calcium ion signaling    Any process that modulates the frequency, rate or extent of skeletal muscle contraction by changing the calcium ion signals that trigger contraction.
    GO:0002028    regulation of sodium ion transport    Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051823    regulation of synapse structural plasticity    Any process that modulates the frequency, rate or extent of synapse structural plasticity. Synapse structural plasticity is a type of cytoskeletal remodeling; this remodeling is induced by stimuli that can lead to long term potentiation and it can be activity-dependent or -independent. Examples of cytoskeletal changes include the formation of new spines and increase in spine size; this can be accompanied by the insertion of greater numbers of glutamate (or other neurotransmitter) receptors into the post-synaptic membrane.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0031307    integral component of mitochondrial outer membrane    The component of the mitochondrial outer membrane consisting of the gene products 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:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005640    nuclear outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
    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: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.
    GO:0016529    sarcoplasmic reticulum    A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.
    GO:0033017    sarcoplasmic reticulum membrane    The lipid bilayer surrounding the sarcoplasmic reticulum.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DMPK_HUMAN | Q090132vd5

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