Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOTOR DOMAIN OF HUMAN KINESIN FAMILY MEMBER C1
 
Authors :  H. Zhu, W. Tempel, H. He, Y. Shen, J. Wang, G. Brothers, R. Landry, C. H. Ar A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Struct Genomics Consortium (Sgc)
Date :  26 Sep 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin, Structural Genomics Consortium, Motor Domain, Adp, Sgc, Atp- Binding, Cell Cycle, Cell Division, Endosome, Microtubule, Mitosis, Motor Protein, Nucleotide-Binding, Nucleus, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhu, W. Tempel, H. He, Y. Shen, J. Wang, G. Brothers, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Motor Domain Of Human Kinesin Family Member C1.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KIFC1
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPFBOH-LIC
    Expression System StrainHIGHFIVE (INVITROGEN)
    Expression System Taxid7111
    Expression System Vector TypePLASMID
    GeneKIFC1, HSET, KNSL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKINESIN-LIKE PROTEIN 2, KINESIN-RELATED PROTEIN HSET

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3UNX5Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:417 , ADP A:800BINDING SITE FOR RESIDUE MG A 700
2AC2SOFTWAREARG A:316 , ARG A:318 , PRO A:319 , LEU A:321 , THR A:412 , GLY A:413 , SER A:414 , GLY A:415 , LYS A:416 , THR A:417 , PHE A:418 , MG A:700BINDING SITE FOR RESIDUE ADP A 800
3AC3SOFTWAREPHE A:442 , CYS A:509 , GLU A:510BINDING SITE FOR RESIDUE UNX A 1
4AC4SOFTWAREGLY A:425 , GLY A:426 , ASP A:427BINDING SITE FOR RESIDUE UNX A 2
5AC5SOFTWAREHIS A:550 , SER A:551 , SER A:552 , ARG A:553BINDING SITE FOR RESIDUE UNX A 3
6AC6SOFTWAREARG A:436BINDING SITE FOR RESIDUE UNX A 4
7AC7SOFTWAREPRO A:319 , VAL A:320BINDING SITE FOR RESIDUE UNX A 5

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIFC1_HUMAN310-663  1A:310-661
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIFC1_HUMAN559-570  1A:559-570

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003745231aENSE00001946904HSCHR6_MHC_QBL:33288143-33288604462KIFC1_HUMAN1-440--
1.2ENST000003745232ENSE00001696992HSCHR6_MHC_QBL:33294628-33294765138KIFC1_HUMAN5-50460--
1.3ENST000003745233ENSE00001804884HSCHR6_MHC_QBL:33294887-33294986100KIFC1_HUMAN51-84340--
1.5ENST000003745235ENSE00001762221HSCHR6_MHC_QBL:33299911-3329996454KIFC1_HUMAN84-102190--
1.6ENST000003745236ENSE00001745469HSCHR6_MHC_QBL:33300082-3330013251KIFC1_HUMAN102-119180--
1.7cENST000003745237cENSE00002149187HSCHR6_MHC_QBL:33300326-33300726401KIFC1_HUMAN119-2521340--
1.8ENST000003745238ENSE00001689843HSCHR6_MHC_QBL:33301449-33302228780KIFC1_HUMAN253-5122601A:310-512 (gaps)203
1.9aENST000003745239aENSE00001662164HSCHR6_MHC_QBL:33302793-33303083291KIFC1_HUMAN513-609971A:513-609 (gaps)97
1.10ENST0000037452310ENSE00001773034HSCHR6_MHC_QBL:33303189-3330326274KIFC1_HUMAN610-634251A:610-63425
1.11aENST0000037452311aENSE00001628652HSCHR6_MHC_QBL:33303397-3330347276KIFC1_HUMAN634-659261A:634-65926
1.12bENST0000037452312bENSE00001931942HSCHR6_MHC_QBL:33306243-33306509267KIFC1_HUMAN660-673141A:660-6612

(-) 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:289
 aligned with KIFC1_HUMAN | Q9BW19 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:352
                                   319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659  
          KIFC1_HUMAN   310 NIRVFCRVRPVLPGEPTPPPGLLLFPSGPGGPSDPPTRLSLSRSDERRGTLSGAPAPPTRHDFSFDRVFPPGSGQDEVFEEIAMLVQSALDGYPVCIFAYGQTGSGKTFTMEGGPGGDPQLEGLIPRALRHLFSVAQELSGQGWTYSFVASYVEIYNETVRDLLATGTRKGQGGECEIRRAGPGSEELTVTNARYVPVSCEKEVDALLHLARQNRAVARTAQNERSSRSHSVFQLQISGEHSSRGLQCGAPLSLVDLAGSERLDPGLALGPGERERLRETQAINSSLSTLGLVIMALSNKESHVPYRNSKLTYLLQNSLGGSAKMLMFVNISPLEENVSESLNSLRFASKVN 661
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2repA00 A:310-661 Kinesin                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------      ----Kines                 in-2repA01 A:347-661                                                                                                                                                                                                                                                                                  Pfam domains
         Sec.struct. author .eeeeeee..........hhhhh....------....eee..-----------------..eee..eee....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee..eeee.....--------..eee.---...eee.....eee.hhhhhhhhhhhhhhhhhhh.-----hhhhheeeeeeeeeeee.....eeeeeeeeee.....------------------------hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) KINESIN_MOTOR_2  PDB: A:310-661 UniProt: 310-663                                                                                                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.8  PDB: A:310-512 (gaps) UniProt: 253-512 [INCOMPLETE]                                                                                                                                              Exon 1.9a  PDB: A:513-609 (gaps) UniProt: 513-609                                                Exon 1.10  PDB: A:610-634-------------------------1. Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11a  PDB: A:634-659-- Transcript 1 (2)
                 2rep A 310 NIRVFCRVRPVLPGEPTPPPGLLLFPS------DPPTRLSLS-----------------RHDFSFDRVFPPGSGQDEVFEEIAMLVQSALDGYPVCIFAYGQTGSGKTFTMEGGPGGDPQLEGLIPRALRHLFSVAQELSGQGWTYSFVASYVEIYNETVRDLLATG--------CEIRRA---SEELTVTNARYVPVSCEKEVDALLHLARQNRAVAR-----RSSRSHSVFQLQISGEHSSRGLQCGAPLSLVDLAGSE------------------------SLSTLGLVIMALSNKESHVPYRNSKLTYLLQNSLGGSAKMLMFVNISPLEENVSESLNSLRFASKVN 661
                                   319       329      |  -   |   349 |       -       369       379       389       399       409       419       429       439       449       459       469      |  -     | 489|   |  499       509       519        |-    |  539       549       559       569|        -         -     | 599       609       619       629       639       649       659  
                                                    336    343     351               369                                                                                                        476      485  490 494                               528   534                                 570                      595                                                                  

   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 2REP)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KIFC1_HUMAN | Q9BW19)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
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: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:0007080    mitotic metaphase plate congression    The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    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:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rep)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rep
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KIFC1_HUMAN | Q9BW19
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  KIFC1_HUMAN | Q9BW19
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2REP)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2REP)