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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH ADP-MG-VO4
 
Authors :  R. Nitta, M. Kikkawa, Y. Okada, N. Hirokawa
Date :  19 Apr 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin, Microtubule, Motor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Nitta, M. Kikkawa, Y. Okada, N. Hirokawa
Kif1A Alternately Uses Two Loops To Bind Microtubules
Science V. 305 678 2004
PubMed-ID: 15286375  |  Reference-DOI: 10.1126/SCIENCE.1096621
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (FUSION PROTEIN CONSISTING OF KINESIN- LIKE PROTEIN KIF1A, KINESIN HEAVY CHAIN ISOFORM 5C AND A HIS TAG
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMOTOR DOMAIN OF KINESIN-LIKE PROTEIN KIF1A AND RESIDUES 329-334 OF KINESIN HEAVY CHAIN ISOFORM 5C
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsFUSION PROTEIN COMPRISES RESIDUES 1-355 OF KINESIN-LIKE PROTEIN KIF1A, AND RESIDUES 329-334 OF KINESIN HEAVY CHAIN ISOFORM 5C, AND C-TERMINAL TAIL WITH SEQUENCE HHHHH
    SynonymAXONAL TRANSPORTER OF SYNAPTIC VESICLES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3VO41Ligand/IonVANADATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:72 , MET A:210 , GLU A:212 , ARG A:216 , GLY A:262 , HOH A:581 , HOH A:613 , HOH A:625BINDING SITE FOR RESIDUE VO4 A 400
2AC2SOFTWARESER A:104 , ADP A:500 , HOH A:502 , HOH A:594 , HOH A:595 , HOH A:596BINDING SITE FOR RESIDUE MG A 501
3AC3SOFTWAREARG A:11 , ARG A:13 , SER A:58 , GLU A:63 , ASP A:64 , ILE A:65 , TYR A:67 , THR A:99 , GLY A:100 , ALA A:101 , GLY A:102 , LYS A:103 , SER A:104 , TYR A:105 , MG A:501 , HOH A:502 , HOH A:549 , HOH A:583 , HOH A:589 , HOH A:594 , HOH A:596 , HOH A:645BINDING SITE FOR RESIDUE ADP A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:234 -Asn A:235
2Ala A:260 -Lys A:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIF1A_MOUSE5-354  1A:5-353
KIF5C_MOUSE8-327  1A:5-352
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIF5C_MOUSE226-237  1A:243-253
KIF1A_MOUSE242-253  1A:242-253

(-) Exons   (0, 0)

(no "Exon" information available for 1VFZ)

(-) 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:338
 aligned with KIF1A_MOUSE | P33173 from UniProtKB/Swiss-Prot  Length:1695

    Alignment length:350
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
          KIF1A_MOUSE     4 ASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPRTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQ 353
               SCOP domains d1vfza_ A: Kinesin                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1vfzA00 A:4-353 Kinesin                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------Kinesin-1vfzA01 A:11-353                                                                                                                                                                                                                                                                                                                                Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhh.....eeee..eeee..........eeee..eeee...........hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhh........hhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeee...........eeee...eeee.....ee..hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee.--...eeeeeeeeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.----------..hhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -KINESIN_MOTOR_2  PDB: A:5-353 UniProt: 5-354                                                                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO---------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfz A   4 ASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPRTVAATNMNETSSRSHAVFNIIFTQKRHD--TNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGP----------FIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQ 353
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       | -|      243       253       263       273       283        |-       303       313       323       333       343       353
                                                                                                                                                                                                                                                             231  |                                                       292        303                                                  
                                                                                                                                                                                                                                                                234                                                                                                                       

Chain A from PDB  Type:PROTEIN  Length:338
 aligned with KIF5C_MOUSE | P28738 from UniProtKB/Swiss-Prot  Length:956

    Alignment length:340
                                                                                                                                                             123                          151                                                                                                                               277                                                 
                                                                  46     47                         74       75                                            122 |                        150 |                                                                 219 220                                                     276 |                                                 
                                    16        26        36        46      | 50        60        70   |     -  |     82        92       102       112       122 |     131       141        |-|      160       170       180       190       200       210        |-  |    227       237       247       257       267        |-|      286       296       306       316       326
          KIF5C_MOUSE     7 CSIKVMCRFRPLNEAEILRGDKFIPKFKGEETVVIGQGKP------YVFDRVLPPNTTQEQVYNACAKQIVKDV--------LEGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIAHDIFDHIYS-MDENLEFHIKVSYFEIYLDKIRDLLDVS-KTNLAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVE---TEKKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGTKTH-VPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAKT 326
               SCOP domains d1vfza_ A: Kinesin                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vfzA00 A:4-353 Kinesin                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------Kinesin-1vfzA01 A:11-353                                                                                                                                                                                                                                                                                                                      Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhh.....eeee..eeee..........eeee..eeee...........hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhh.......-.hhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeee...........eeee...eeee.....ee..hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee....eeeeee-eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -KINESIN_MOTOR_2  PDB: A:5-352 UniProt: 8-327                                                                                                                                                                                                                                                                                                        PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfz A   4 ASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQ-QGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPRTVAATNMNETSSRSHAVFNIIFTQKRHDTNITTEKVS-KISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQ 353
                                    13        23        33        43        53        63        73        83        93       103       113 | |   122       132       142       152       162       172       182       192       202       212       222       234       243       253       263       273       283       303       313       323       333       343       353
                                                                                                                                         115 |                                                                                                                231|     242 |                                              292|                                                  
                                                                                                                                           116                                                                                                                 234       243                                               303                                                  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KIF5C_MOUSE | P28738)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008574    ATP-dependent microtubule motor activity, plus-end-directed    Catalysis of movement along a microtubule toward the plus end, coupled to the hydrolysis of ATP.
    GO:0034190    apolipoprotein receptor binding    Interacting selectively and non-covalently with an apolipoprotein receptor.
    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).
biological process
    GO:0030705    cytoskeleton-dependent intracellular transport    The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
    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: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:0008045    motor neuron axon guidance    The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0035253    ciliary rootlet    A cytoskeleton-like structure, originating from the basal body at the proximal end of a cilium, and extending proximally toward the cell nucleus. Rootlets are typically 80-100 nm in diameter and contain cross striae distributed at regular intervals of approximately 55-70 nm.
    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: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: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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

Chain A   (KIF1A_MOUSE | P33173)
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:0030705    cytoskeleton-dependent intracellular transport    The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
    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.
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: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: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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KIF1A_MOUSE | P331731i5s 1i6i 1ia0 1vfv 1vfw 1vfx 2hxf 2hxh 2zfi 2zfj 2zfk 2zfl 2zfm
        KIF5C_MOUSE | P287381vfv 1vfw 1vfx 2zfi 2zfj 2zfk 2zfl 2zfm 3j6h 3wrd 3x2t

(-) Related Entries Specified in the PDB File

1vfv KIF1A MOTOR DOMAIN COMPLEXED WITH MG-AMPPNP
1vfw KIF1A MOTOR DOMAIN COMPLEXED WITH MG-AMPPNP
1vfx KIF1A MOTOR DOMAIN COMPLEXED WITH ADP-MG-ALFX