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(-) Description

Title :  STRUCTURAL BASIS OF MICROTUBULE PLUS END TRACKING BY XMAP215, CLIP-170 AND EB1
 
Authors :  K. C. Slep, R. D. Vale
Date :  09 Jul 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Calponin Homology Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. C. Slep, R. D. Vale
Structural Basis Of Microtubule Plus End Tracking By Xmap215, Clip-170, And Eb1.
Mol. Cell V. 27 976 2007
PubMed-ID: 17889670  |  Reference-DOI: 10.1016/J.MOLCEL.2007.07.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN BIM1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21 DE3 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCALPONIN HOMOLOGY DOMAIN
    GeneBIM1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QJX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QJX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QJX)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YER016W1YER016W.1V:188276-1893101035BIM1_YEAST1-3443441A:8-124117

(-) 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:117
 aligned with BIM1_YEAST | P40013 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:117
                                    17        27        37        47        57        67        77        87        97       107       117       
           BIM1_YEAST     8 SRTELLTWLNGLLNLNYKKIEECGTGAAYCQIMDSIYGDLPMNRVKFNATAEYEFQTNYKILQSCFSRHGIEKTVYVDKLIRCKFQDNLEFLQWLKKHWIRHKDESVYDPDARRKYR 124
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qjxA00 A:8-124 Actin-binding Protein, T-fimbrin; domain 1                                                            CATH domains
               Pfam domains -CH-2qjxA01 A:9-107                                                                                 ----------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:8-124 UniProt: 1-344 [INCOMPLETE]                                                                    Transcript 1
                 2qjx A   8 SRTELLTWLNGLLNLNYKKIEECGTGAAYCQImDSIYGDLPmNRVKFNATAEYEFQTNYKILQSCFSRHGIEKTVYVDKLIRCKFQDNLEFLQWLKKHWIRHKDESVYDPDARRKYR 124
                                    17        27        37  |     47 |      57        67        77        87        97       107       117       
                                                           40-MSE   49-MSE                                                                       

   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 2QJX)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: CH (43)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BIM1_YEAST | P40013)
molecular function
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0007019    microtubule depolymerization    The removal of tubulin heterodimers from one or both ends of a microtubule.
    GO:0007020    microtubule nucleation    The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
    GO:0007064    mitotic sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission.
    GO:0031578    mitotic spindle orientation checkpoint    A cell cycle checkpoint that monitors and signals errors in the placement or orientation of the spindle in the cell. This delays the completion of anaphase until errors are corrected.
    GO:0007026    negative regulation of microtubule depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
    GO:0030473    nuclear migration along microtubule    The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins.
    GO:0031116    positive regulation of microtubule polymerization    Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    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:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0035371    microtubule plus-end    The growing (plus) end of a microtubule. In vitro, microtubules polymerize more quickly at the plus end than at the minus end. In vivo, microtubule growth occurs only at the plus end, and the plus end switches between periods of growth and shortening, a behavior known as dynamic instability.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0051233    spindle midzone    The area in the center of the spindle where the spindle microtubules from opposite poles overlap.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
    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
        BIM1_YEAST | P400134e61

(-) Related Entries Specified in the PDB File

2qjz 2qk0 2qk1 2qk2