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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE SL-NANDP BOUND AT THE NUCLEOTIDE SITE
 
Authors :  N. Naber, T. J. Minehardt, S. Rice, X. Chen, J. Grammer, M. Matuska, R. D. Vale, P. A. Kollman, R. Car, R. G. Yount, R. Cooke, E. Pate
Date :  01 Apr 04  (Deposition) - 27 Apr 04  (Release) - 18 May 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Ncd, Epr Probe, Model, Switch 1, Microtubule Motor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Naber, T. J. Minehardt, S. Rice, X. Chen, J. Grammer, M. Matuska, R. D. Vale, P. A. Kollman, R. Car, R. G. Yount, R. Cooke, E. Pate
Closing Of The Nucleotide Pocket Of Kinesin-Family Motors Upon Binding To Microtubules
Science V. 300 798 2003
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLARET SEGREGATIONAL PROTEIN
    ChainsA
    FragmentMOTOR DOMAIN
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    SynonymNCD

 Structural Features

(-) Chains, Units

  
Theoretical Model 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Theoretical Model (3, 7)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NA5Ligand/IonSODIUM ION
3SLN1Ligand/Ion1-(4-AZIDO-2-NITROPHENYL)AMINO-3-(1-OXYL-2,2,5,5-TETRAMETHYLPYRROLIDINYL-3-CARBAMIDO)-2-PROPYLDISPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1SYP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.NCD_DROME348-670  1A:348-667
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.NCD_DROME574-585  1A:574-585

(-) Exons   (0, 0)

(no "Exon" information available for 1SYP)

(-) Sequences/Alignments

Theoretical Model
   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:323
 aligned with NCD_DROME | P20480 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:323
                                   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664   
            NCD_DROME   345 LRGNIRVFCRIRPPLESEENRMCCTWTYHDESTVELQSIDAQAKSKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRNLGWEYEIKATFLEIYNEVLYDLLSNEQKDMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSESPKTSTRMTETKNINRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV 667
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhh.....eeeeee..eeeee..............ee..eee......hhhhhh.hhhhhhhhh..eeeeeeee............hhhhhhhhhhhhhhhhhhhhhhh....ee..eeeeeee....eee..........ee.........ee.....ee..hhhhhhhhhhhhhhh...............eeeeeeeeeee......eeeeeeeeee........eeee..eeee.hhhhhhhhhhhhhhhh.........hhhhhhhhhhh......eeeeee.....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---KINESIN_MOTOR_2  PDB: A:348-667 UniProt: 348-670                                                                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO---------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1syp A 345 LRGNIRVFCRIRPPLESEENRMCCTWTYHDESTVELQSIDAQAKSKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRNLGWEYEIKATFLEIYNEVLYDLLSNEQKDMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSESPKTSTRMTETKNINRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV 667
                                   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664   

   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 1SYP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1SYP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SYP)

(-) Gene Ontology  (40, 40)

Theoretical Model(hide GO term definitions)
Chain A   (NCD_DROME | P20480)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008569    ATP-dependent microtubule motor activity, minus-end-directed    Catalysis of movement along a microtubule toward the minus end, coupled to the hydrolysis of ATP.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0051298    centrosome duplication    The replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0032837    distributive segregation    The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during a normally chiasmate meiosis under the condition that chiasma have not occurred between a particular pair of homologs. Distributive segregation is a "backup" mechanism to ensure the segregation of homologs that have failed to cross over - either as a consequence of mutation or not, as, for example, the 4th chromosome of Drosophila melanogaster (which never exchanges, presumably due to its small size) - but nevertheless segregate normally.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0000212    meiotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle.
    GO:0001578    microtubule bundle formation    A process that results in a parallel arrangement of microtubules.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0031534    minus-end directed microtubule sliding    The movement of one microtubule along another microtubule, where the motion is directed towards the minus ends of the microtubules.
    GO:0007100    mitotic centrosome separation    Separation of duplicated centrosome components at the beginning of mitosis. The centriole pair within each centrosome becomes part of a separate microtubule organizing center that nucleates a radial array of microtubules called an aster. The two asters move to opposite sides of the nucleus to form the two poles of the mitotic spindle.
    GO:0090307    mitotic spindle assembly    The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis.
    GO:0000022    mitotic spindle elongation    The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
    GO:1901673    regulation of mitotic spindle assembly    Any process that modulates the frequency, rate or extent of mitotic spindle assembly.
    GO:0032888    regulation of mitotic spindle elongation    Any process that modulates the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle.
    GO:0007056    spindle assembly involved in female meiosis    The aggregation, arrangement and bonding together of a set of components to form the spindle during a meiotic cell cycle in females. An example of this is found in Drosophila melanogaster.
    GO:0090306    spindle assembly involved in meiosis    The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of meiosis.
    GO:0007051    spindle 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, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0030981    cortical microtubule cytoskeleton    The portion of the microtubule 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:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    GO:0072687    meiotic spindle    A spindle that forms as part of meiosis. Several proteins, such as budding yeast Spo21p, fission yeast Spo2 and Spo13, and C. elegans mei-1, localize specifically to the meiotic spindle and are absent from the mitotic spindle.
    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:0005872    minus-end kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the minus end of a microtubule.
    GO:1990498    mitotic spindle microtubule    Any microtubule that is part of a mitotic spindle; anchored at one spindle pole.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCD_DROME | P204801cz7 1n6m 1ozx 1syj 1sz4 1sz5 2ncd 3l1c 3u06 5hle 5hnw 5hnx 5hny 5hnz

(-) Related Entries Specified in the PDB File

1ozx MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND WITH ADP BOUND AT THE NUCLEOTIDE SITE
1syj MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE SSL-NANDP BOUND AT THE NUCLEOTIDE SITE
1sz4 MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE 2' -SLADP BOUND AT THE NUCLEOTIDE SITE
1sz5 MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE 3' -SLADP BOUND AT THE NUCLEOTIDE SITE