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(-) Description

Title :  NMR STRUCTURE OF THE HUMAN DEMATIN HEADPIECE DOMAIN
 
Authors :  B. S. Frank, D. Vardar, A. H. Chishti, C. J. Mcknight
Date :  17 Sep 03  (Deposition) - 23 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (13x)
Keywords :  Dematin Headpiece, Villin Headpiece, Actin Binding Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. S. Frank, D. Vardar, A. H. Chishti, C. J. Mcknight
The Nmr Structure Of Dematin Headpiece Reveals A Dynamic Loop That Is Conformationally Altered Upon Phosphorylation At A Distal Site
J. Biol. Chem. V. 279 7909 2004
PubMed-ID: 14660664  |  Reference-DOI: 10.1074/JBC.M310524200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEMATIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PD48
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  
NMR Structure (13x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QZP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HPPS51089 Headpiece (HP) domain profile.DEMA_HUMAN337-405  1A:13-76

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7aENST000003582427aENSE00001530792chr8:21916686-21917007322DEMA_HUMAN-00--
1.8dENST000003582428dENSE00002177879chr8:21924216-21924404189DEMA_HUMAN1-660--
1.9ENST000003582429ENSE00001719675chr8:21924596-2192467075DEMA_HUMAN7-31250--
1.10bENST0000035824210bENSE00001592346chr8:21925038-21925193156DEMA_HUMAN32-83520--
1.11bENST0000035824211bENSE00001158939chr8:21926527-2192657145DEMA_HUMAN84-98150--
1.11gENST0000035824211gENSE00001158933chr8:21926930-21927029100DEMA_HUMAN99-132340--
1.12ENST0000035824212ENSE00001158927chr8:21927392-2192744857DEMA_HUMAN132-151200--
1.13dENST0000035824213dENSE00001158922chr8:21927693-21927845153DEMA_HUMAN151-202520--
1.14ENST0000035824214ENSE00001158916chr8:21929837-21929961125DEMA_HUMAN202-243420--
1.15ENST0000035824215ENSE00001158910chr8:21931241-21931346106DEMA_HUMAN244-279360--
1.16ENST0000035824216ENSE00000980119chr8:21937691-2193775565DEMA_HUMAN279-300220--
1.17aENST0000035824217aENSE00000980120chr8:21937923-2193797149DEMA_HUMAN301-317171A:9-102
1.19ENST0000035824219ENSE00001688893chr8:21938306-219383105DEMA_HUMAN317-31821A:10-112
1.20aENST0000035824220aENSE00001649118chr8:21938313-2193838169DEMA_HUMAN319-341231A:12-121
1.21ENST0000035824221ENSE00002163994chr8:21938624-2193870481DEMA_HUMAN342-368271A:13-3927
1.22dENST0000035824222dENSE00001329702chr8:21938861-219400351175DEMA_HUMAN369-405371A:40-7637

(-) 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:68
 aligned with DEMA_HUMAN | Q08495 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:90
                                   325       335       345       355       365       375       385       395       405
           DEMA_HUMAN   316 PGLQNGEGQRGRMDRGNSLPCVLEQKIYPYEMLVVTNKGRTKLPPGVDRMRLERHLSAEDFSRVFAMSPEEFGKLALWKRNELKKKASLF 405
               SCOP domains d1qz                      pa_ A: Dematin                                                   SCOP domains
               CATH domains 1qzp                      A00 A:9-76 Villin Headpiece Domain; Chain A                      CATH domains
               Pfam domains ------------------------------------------------------VHP-1qzpA01 A:41-76                  Pfam domains
         Sec.struct. author ....----------------------.....................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------HP  PDB: A:13-76 UniProt: 337-405                                     PROSITE
           Transcript 1 (1) 1.-Exon 1.20a  PDB: A:12-1Exon 1.21  PDB: A:13-39    Exon 1.22d  PDB: A:40-76              Transcript 1 (1)
           Transcript 1 (2) -1.--------------------------------------------------------------------------------------- Transcript 1 (2)
                 1qzp A   9 PGLQ----------------------IYPYEMLVVTNKGRTKLPPGVDRMRLERHLSAEDFSRVFAMSPEEFGKLALWKRNELKKKASLF  76
                               |     -         -      | 16        26        36        46        56        66        76
                              12                     13
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: VHP] (23)

(-) Gene Ontology  (49, 49)

NMR Structure(hide GO term definitions)
Chain A   (DEMA_HUMAN | Q08495)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
biological process
    GO:0030036    actin 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 comprising actin filaments and their associated proteins.
    GO:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    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:0090527    actin filament reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of actin filaments.
    GO:0035585    calcium-mediated signaling using extracellular calcium source    A series of molecular signals in which a cell uses calcium ions imported from an extracellular source to convert a signal into a response.
    GO:0035584    calcium-mediated signaling using intracellular calcium source    A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response.
    GO:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0071277    cellular response to calcium ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    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:0048821    erythrocyte development    The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
    GO:0010812    negative regulation of cell-substrate adhesion    Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0051895    negative regulation of focal adhesion assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0010801    negative regulation of peptidyl-threonine phosphorylation    Any process that decreases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0050732    negative regulation of peptidyl-tyrosine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0090315    negative regulation of protein targeting to membrane    Any process that decreases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:1900025    negative regulation of substrate adhesion-dependent cell spreading    Any process that stops, prevents or reduces the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0010763    positive regulation of fibroblast migration    Any process that increases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
    GO:2001046    positive regulation of integrin-mediated signaling pathway    Any process that activates or increases the frequency, rate or extent of integrin-mediated signaling pathway.
    GO:1901731    positive regulation of platelet aggregation    Any process that activates or increases the frequency, rate or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:1900026    positive regulation of substrate adhesion-dependent cell spreading    Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:0090303    positive regulation of wound healing    Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0070560    protein secretion by platelet    The regulated release of proteins by a platelet or group of platelets.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051489    regulation of filopodium assembly    Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0010591    regulation of lamellipodium assembly    Any process that modulates the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
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:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031253    cell projection membrane    The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
    GO:0030863    cortical cytoskeleton    The portion of the cytoskeleton that lies just beneath the plasma membrane.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0031095    platelet dense tubular network membrane    The lipid bilayer surrounding the platelet dense tubular network.
    GO:0014731    spectrin-associated cytoskeleton    The part of the cytoskeleton composed of spectrin, protein 4.1 and ankyrin. Spectrin-associated cytoskeleton is associated with the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEMA_HUMAN | Q08495: 1zv6

(-) Related Entries Specified in the PDB File

1qqv NMR STRUCTURE OF THE HEADPIECE DOMAIN OF CHICKEN VILLIN
1vii NMR STRUCTURE OF THE THERMOSTABLE, 35-RESIDUE SUBDOMAIN FROM CHICKEN VILLIN HEADPIECE