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

(-) Description

Title :  CRYSTAL STRUCTURES OF MUTANTS REVEAL A SIGNALLING PATHWAY FOR ACTIVATION OF THE KINESIN MOTOR ATPASE
 
Authors :  M. Yun, X. Zhang, C. G. Park, H. W. Park, S. A. Endow
Date :  11 Jul 00  (Deposition) - 13 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kar3, Kinesin-Related Protein, Motor Protein, Microtubule Binding Protein, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yun, X. Zhang, C. G. Park, H. W. Park, S. A. Endow
A Structural Pathway For Activation Of The Kinesin Motor Atpase.
Embo J. V. 20 2611 2001
PubMed-ID: 11387196  |  Reference-DOI: 10.1093/EMBOJ/20.11.2611
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KAR3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentE631A MUTANT MOTOR DOMAIN
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsSACCHAROMYCES CEREVISIAE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:481 , ADP A:998BINDING SITE FOR RESIDUE MG A 996
2AC2SOFTWARETHR B:481 , ADP B:999BINDING SITE FOR RESIDUE MG B 997
3AC3SOFTWAREARG A:392 , ARG A:394 , PRO A:395 , GLN A:475 , THR A:476 , GLY A:477 , SER A:478 , GLY A:479 , LYS A:480 , THR A:481 , PHE A:482 , MG A:996 , HOH A:1003BINDING SITE FOR RESIDUE ADP A 998
4AC4SOFTWAREARG B:392 , ARG B:394 , PRO B:395 , GLN B:475 , THR B:476 , GLY B:477 , SER B:478 , GLY B:479 , LYS B:480 , THR B:481 , PHE B:482 , MG B:997 , HOH B:1050BINDING SITE FOR RESIDUE ADP B 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F9W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F9W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 12)

Asymmetric/Biological Unit (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_KAR3_YEAST_002 *S462LKAR3_YEAST  ---  ---A/BS462L
2UniProtVAR_KAR3_YEAST_003 *E521DKAR3_YEAST  ---  ---A/BE521D
3UniProtVAR_KAR3_YEAST_004 *R550SKAR3_YEAST  ---  ---A/BR550S
4UniProtVAR_KAR3_YEAST_005 *T558AKAR3_YEAST  ---  ---A/BT558A
5UniProtVAR_KAR3_YEAST_006 *N650KKAR3_YEAST  ---  ---A/BN650K
6UniProtVAR_KAR3_YEAST_007 *V659LKAR3_YEAST  ---  ---A/BV659L
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KAR3_YEAST386-723
 
  2A:386-722
B:386-722
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KAR3_YEAST620-631
 
  2A:620-630
B:620-630

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR141C1YPR141C.1XVI:817919-8157302190KAR3_YEAST1-7297292A:385-722 (gaps)
B:385-722 (gaps)
338
338

(-) 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:300
 aligned with KAR3_YEAST | P17119 from UniProtKB/Swiss-Prot  Length:729

    Alignment length:338
                                   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       674       684       694       704       714        
           KAR3_YEAST   385 GNIRVYCRIRPALKNLENSDTSLINVNEFDDNSGVQSMEVTKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPGDGIIPSTISHIFNWINKLKTKGWDYKVNCEFIEIYNENIVDLLRSDNNNKEDTSIGLKHEIRHDQETKTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQPDSTKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVNS 722
               SCOP domains d1f9wa_ A: Kinesi  n motor Ncd (non-clare       t disjunctional)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1f9wA00 A:385-722   Kinesin                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........--.................eeee.-------.eeee.........hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..eee....------------....eeee....eeee.....ee..hhhhhhhhhhhhhhhhh.-------hhhhheeeeeeeeee........eeeeeeeee......----------.hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------L----------------------------------------------------------D----------------------------S-------A-------------------------------------------------------------------------------------------K--------L--------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -KINESIN_MOTOR_2  PDB: A:386-722 UniProt: 386-723                                                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:385-722 (gaps) UniProt: 1-729 [INCOMPLETE]                                                                                                                                                                                                                                                                                        Transcript 1
                 1f9w A 385 GNIRVYCRIRPALKNLE--DTSLINVNEFDDNSGVQSMEVT-------VHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPGDGIIPSTISHIFNWINKLKTKGWDYKVNCEFIEIYNENIVDLLR------------LKHEIRHDQETKTTTITNVTSCKLESEEMVEIILKKANKLRST-------HSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSAR----------LRETQNINKSLSCLGDVIHALGQPDSTKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVNS 722
                                   394      |404       414       424|      434       444       454       464       474       484       494       504       514       524       | -         -|      554       564       574       584  |      -|      604       614       624       | -       644       654       664       674       684       694       704       714        
                                          401  |                  425     433                                                                                                532          545                                       587     595                                  632        643                                                                               
                                             404                                                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with KAR3_YEAST | P17119 from UniProtKB/Swiss-Prot  Length:729

    Alignment length:338
                                   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       674       684       694       704       714        
           KAR3_YEAST   385 GNIRVYCRIRPALKNLENSDTSLINVNEFDDNSGVQSMEVTKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPGDGIIPSTISHIFNWINKLKTKGWDYKVNCEFIEIYNENIVDLLRSDNNNKEDTSIGLKHEIRHDQETKTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQPDSTKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVNS 722
               SCOP domains d1f9wb_ B: Kinesi  n motor Ncd (non-clare       t disjunctional)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1f9wB00 B:385-722   Kinesin                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........--.................eeee.-------.eeee.........hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..eee....------------....eeee....eeee.....ee..hhhhhhhhhhhhhhhhh.-------hhhhheeeeeeeeee........eeeeeeeee......----------.hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------L----------------------------------------------------------D----------------------------S-------A-------------------------------------------------------------------------------------------K--------L--------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -KINESIN_MOTOR_2  PDB: B:386-722 UniProt: 386-723                                                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:385-722 (gaps) UniProt: 1-729 [INCOMPLETE]                                                                                                                                                                                                                                                                                        Transcript 1
                 1f9w B 385 GNIRVYCRIRPALKNLE--DTSLINVNEFDDNSGVQSMEVT-------VHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPGDGIIPSTISHIFNWINKLKTKGWDYKVNCEFIEIYNENIVDLLR------------LKHEIRHDQETKTTTITNVTSCKLESEEMVEIILKKANKLRST-------HSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSAR----------LRETQNINKSLSCLGDVIHALGQPDSTKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVNS 722
                                   394      |404       414       424|      434       444       454       464       474       484       494       504       514       524       | -         -|      554       564       574       584  |      -|      604       614       624       | -       644       654       664       674       684       694       704       714        
                                          401  |                  425     433                                                                                                532          545                                       587     595                                  632        643                                                                               
                                             404                                                                                                                                                                                                                                                                                                                              

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F9W)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KAR3_YEAST | P17119)
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: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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
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:0000741    karyogamy    The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.
    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: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: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:0000743    nuclear migration involved in conjugation with cellular fusion    The microtubule-based movement of nuclei towards one another as a prelude to karyogamy in organisms undergoing conjugation with cellular fusion.
    GO:0060236    regulation of mitotic spindle organization    Any process that modulates the rate, frequency or extent of the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
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: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:0005816    spindle pole body    The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.

 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 ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f9w)
 

(-) 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
  1f9w
    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
  KAR3_YEAST | P17119
    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
  KAR3_YEAST | P17119
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KAR3_YEAST | P171191f9t 1f9u 1f9v 3kar 4etp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1F9W)