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(-) Description

Title :  SOLUTION STRUCTURE OF CALPONIN HOMOLOGY DOMAIN OF HUMAN MICAL-1
 
Authors :  H. Sun, H. Dai, J. Zhang, S. Xiong, J. Wu, Y. Shi
Date :  07 Apr 06  (Deposition) - 19 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Helix, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Sun, H. Dai, J. Zhang, X. Jin, S. Xiong, J. Xu, J. Wu, Y. Shi
Solution Structure Of Calponin Homology Domain Of Human Mical-1
J. Biomol. Nmr V. 36 295 2006
PubMed-ID: 17043746  |  Reference-DOI: 10.1007/S10858-006-9062-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEDD9-INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidP28
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCALPONIN HOMOLOGY DOMAIN
    GeneMICAL1, MICAL, NICAL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMOLECULE INTERACTING WITH CASL PROTEIN 1, MICAL-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DK9)

(-) Sites  (0, 0)

(no "Site" information available for 2DK9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DK9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DK9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067065R453CMICA1_HUMANPolymorphism17854785AH-6C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.MICA1_HUMAN508-609  1A:3-104

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003588071aENSE00001346540chr6:109777190-109776922269MICA1_HUMAN-00--
1.3ENST000003588073ENSE00002200739chr6:109775442-109775142301MICA1_HUMAN1-86860--
1.4ENST000003588074ENSE00002147354chr6:109775048-109774841208MICA1_HUMAN87-156700--
1.5ENST000003588075ENSE00002143510chr6:109774570-109774466105MICA1_HUMAN156-191360--
1.6aENST000003588076aENSE00002150654chr6:109773818-109773714105MICA1_HUMAN191-226360--
1.7bENST000003588077bENSE00002173557chr6:109773604-109773449156MICA1_HUMAN226-278530--
1.7eENST000003588077eENSE00002190488chr6:109772903-109772803101MICA1_HUMAN278-311340--
1.8ENST000003588078ENSE00002173562chr6:109771760-109771503258MICA1_HUMAN312-397860--
1.9bENST000003588079bENSE00002193439chr6:109771288-109771173116MICA1_HUMAN398-436390--
1.10aENST0000035880710aENSE00002162670chr6:109770986-109770860127MICA1_HUMAN436-478431A:-8--18
1.10cENST0000035880710cENSE00002165722chr6:109770684-10977060382MICA1_HUMAN479-506281A:0-12
1.10eENST0000035880710eENSE00002195022chr6:109770082-109769935148MICA1_HUMAN506-555501A:1-5050
1.10gENST0000035880710gENSE00002198253chr6:109769596-109769406191MICA1_HUMAN555-619651A:50-10960
1.10hENST0000035880710hENSE00002167337chr6:109769166-10976907889MICA1_HUMAN619-648300--
1.10iENST0000035880710iENSE00002171488chr6:109768925-10976888442MICA1_HUMAN649-662140--
1.10jENST0000035880710jENSE00002176586chr6:109768643-10976856084MICA1_HUMAN663-690280--
1.10kENST0000035880710kENSE00002160425chr6:109768432-109768276157MICA1_HUMAN691-743530--
1.11aENST0000035880711aENSE00002166224chr6:109767975-10976789977MICA1_HUMAN743-768260--
1.11eENST0000035880711eENSE00002199952chr6:109767615-109767339277MICA1_HUMAN769-861930--
1.12ENST0000035880712ENSE00002160349chr6:109767065-10976697492MICA1_HUMAN861-891310--
1.13ENST0000035880713ENSE00002201707chr6:109766732-109766619114MICA1_HUMAN892-929380--
1.14ENST0000035880714ENSE00002149641chr6:109766493-10976640094MICA1_HUMAN930-961320--
1.15ENST0000035880715ENSE00002147191chr6:109766198-109766099100MICA1_HUMAN961-994340--
1.16ENST0000035880716ENSE00002173143chr6:109766001-10976592874MICA1_HUMAN994-1019260--
1.17bENST0000035880717bENSE00002190737chr6:109765542-109765265278MICA1_HUMAN1019-1067490--

(-) Sequences/Alignments

NMR Structure
   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:118
 aligned with MICA1_HUMAN | Q8TDZ2 from UniProtKB/Swiss-Prot  Length:1067

    Alignment length:164
                                   460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610    
          MICA1_HUMAN   451 MHRNVAQYGLDPATRYPNLNLRAVTPNQVRDLYDVLAKEPVQRNNDKTDTGMPATGSAGTQEELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVVSAQAVVAGSDPLGLIAYLSHFHSAFKSM 614
               SCOP domains d2dk9a_                                               A: automated matches                                                                                           SCOP domains
               CATH domains -----------------------------------------------------------2dk9A01 A:5-107 Actin-binding Protein, T-fimbrin; domain 1                                             -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........----------------------------------------------.hhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --C----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------CH  PDB: A:3-104 UniProt: 508-609                                                                     ----- PROSITE
           Transcript 1 (1) Exon 1.10a  PDB: A:-8--1    Exon 1.10c  PDB: A:0-1      ------------------------------------------------Exon 1.10g  PDB: A:50-109 UniProt: 555-619 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.10e  PDB: A:1-50 UniProt: 506-555          ----------------------------------------------------------- Transcript 1 (2)
                 2dk9 A  -8 MGHHHHHH----------------------------------------------MGSAGTQEELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVVSAQAVVAGSDPLGLIAYLSHFHSAFKSM 109
                                   | -         -         -         -         -    |    5        15        25        35        45        55        65        75        85        95       105    
                                  -1                                              0                                                                                                             

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DK9)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (MICA1_HUMAN | Q8TDZ2)
molecular function
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016709    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030042    actin filament depolymerization    Disassembly of actin filaments by the removal of actin monomers from a filament.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0019417    sulfur oxidation    The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur.
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:0005882    intermediate filament    A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MICA1_HUMAN | Q8TDZ21wyl 2co8 5le0 5lpn

(-) Related Entries Specified in the PDB File

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