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(-) Description

Title :  SOLUTION STRUCTURE OF THE APO N-TERMINAL DOMAIN OF YEAST CALMODULIN
 
Authors :  H. Ishida, K. Takahashi, K. Nakashima, Y. Kumaki, M. Nakata, K. Hikichi, M. Yazawa
Date :  13 Jun 00  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Ef-Hand, Helix-Loop-Helix, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Ishida, K. Takahashi, K. Nakashima, Y. Kumaki, M. Nakata, K. Hikichi, M. Yazawa
Solution Structures Of The N-Terminal Domain Of Yeast Calmodulin: Ca2+-Dependent Conformational Change And Its Functional Implication
Biochemistry V. 39 13660 2000
PubMed-ID: 11076504  |  Reference-DOI: 10.1021/BI000582X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALMODULIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-30B(+) AND PIC10
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsINTRACELLULAR CALCIUM SENSOR

 Structural Features

(-) Chains, Units

  
NMR Structure (30x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F54)

(-) Sites  (0, 0)

(no "Site" information available for 1F54)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F54)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F54)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F54)

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM_YEAST8-43
44-79
81-116
  2A:7-42
A:43-77
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM_YEAST21-33
57-69
94-106
  2A:20-32
A:56-68
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR109C1YBR109C.1II:458356-457913444CALM_YEAST1-1471471A:1-7777

(-) 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:77
 aligned with CALM_YEAST | P06787 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:77
                                    11        21        31        41        51        61        71       
            CALM_YEAST    2 SSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLK 78
               SCOP domains d1f54a_ A: Calmodulin                                                         SCOP domains
               CATH domains 1f54A00 A:1-77 EF-hand                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh......eeehhhhhhhhhhhh...hhhhhhhhhhh.......eeehhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-77             PROSITE (1)
                PROSITE (2) -------------------EF_HAND_1    -----------------------EF_HAND_1    --------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-77 UniProt: 1-147 [INCOMPLETE]                             Transcript 1
                  1f54 A  1 SSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDGNHQIEFSEFLALMSRQLK 77
                                    10        20        30        40        50        60        70       

   Legend:   → Mismatch (orange background)
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  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 1F54)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (CALM_YEAST | P06787)
molecular function
    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).
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0007114    cell budding    A form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell.
    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:0000742    karyogamy involved in conjugation with cellular fusion    During sexual reproduction, the creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. This occurs after cytogamy.
    GO:0016237    lysosomal microautophagy    The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
    GO:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0051300    spindle pole body organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle pole body (SPB). The SPB is the microtubule organizing center in fungi, and is functionally homologous to the animal cell centrosome.
    GO:0042991    transcription factor import into nucleus    The directed movement of a transcription factor from the cytoplasm to the nucleus.
    GO:0042144    vacuole fusion, non-autophagic    The fusion of two vacuole membranes to form a single vacuole.
cellular component
    GO:0005935    cellular bud neck    The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
    GO:0005934    cellular bud tip    The end of a cellular bud distal to the site of attachment to the mother cell.
    GO:0005823    central plaque of spindle pole body    One of three laminate structures that form the spindle pole body; the central plaque is embedded in the nuclear envelope.
    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:0000131    incipient cellular bud site    The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
    GO:0043332    mating projection tip    The apex of the mating projection in unicellular fungi exposed to mating pheromone; site of polarized growth.
    GO:0005816    spindle pole body    The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CALM_YEAST | P067871f55 1lkj 2lhh 2lhi

(-) Related Entries Specified in the PDB File

1f55 1F55 CONTAINS THE SAME PROTEIN WITH CALCIUM