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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOTOR DOMAIN OF HUMAN KINESIN FAMILY MEMBER 22
 
Authors :  H. Zhu, Y. Shen, W. Tempel, E. Dobrovetsky, F. Mackenzie, C. H. Arrowsmi A. M. Edwards, J. Weigelt, A. Bochkarev, H. Park, Structural Genomic Consortium (Sgc)
Date :  22 Nov 07  (Deposition) - 04 Dec 07  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Limited Proteolysis, Kinesin, Structural Genomics Consortium, Motor Domain, Adp, Sgc, Atp-Binding, Dna-Binding, Microtubule, Motor Protein, Nucleotide-Binding, Nucleus, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhu, Y. Shen, W. Tempel, E. Dobrovetsky, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Motor Domain Of Human Kinesin Family Member 22.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KIF22
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)CODON(+)RIL
    Expression System Taxid562
    GeneKIF22, KID, KNSL4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKINESIN-LIKE DNA-BINDING PROTEIN, KINESIN-LIKE PROTEIN 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3UNK9Mod. Amino Acid
4UNX8Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:134 , ADP A:802 , HOH A:827 , HOH A:828 , HOH A:834BINDING SITE FOR RESIDUE MG A 801
02AC2SOFTWAREARG A:43 , VAL A:44 , ASP A:91BINDING SITE FOR RESIDUE UNX A 701
03AC3SOFTWAREGLN A:89 , MET A:152BINDING SITE FOR RESIDUE UNX A 702
04AC4SOFTWAREASP A:200 , CYS A:201 , ARG A:202 , THR A:299BINDING SITE FOR RESIDUE UNX A 703
05AC5SOFTWAREARG A:45 , ARG A:97BINDING SITE FOR RESIDUE UNX A 704
06AC6SOFTWAREGLN A:119 , ASN A:120 , SER A:336 , ALA A:337BINDING SITE FOR RESIDUE UNX A 705
07AC7SOFTWAREGLN A:101 , ARG A:364BINDING SITE FOR RESIDUE UNX A 706
08AC8SOFTWAREGLU A:178 , TYR A:180BINDING SITE FOR RESIDUE UNX A 707
09AC9SOFTWAREARG A:159 , SER A:217 , PHE A:218BINDING SITE FOR RESIDUE UNX A 708
10BC1SOFTWAREARG A:49 , ARG A:51 , PRO A:52 , PRO A:128 , THR A:129 , GLY A:130 , ALA A:131 , GLY A:132 , LYS A:133 , THR A:134 , HIS A:135 , MG A:801 , HOH A:805 , HOH A:828 , HOH A:834BINDING SITE FOR RESIDUE ADP A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BFN)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:261 -Pro A:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067345P148LKIF22_HUMANDisease (SEMDJL2)193922921AP148L
2UniProtVAR_067346P148SKIF22_HUMANDisease (SEMDJL2)193922920AP148S
3UniProtVAR_067347R149LKIF22_HUMANDisease (SEMDJL2)193922922AR149L
4UniProtVAR_067348R149QKIF22_HUMANDisease (SEMDJL2)193922922AR149Q

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIF22_HUMAN43-368  1A:43-368
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIF22_HUMAN268-279  1A:268-279

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000001608271aENSE00001544520chr16:29802041-29802150110KIF22_HUMAN1-24240--
1.2ENST000001608272ENSE00001668296chr16:29808214-29808409196KIF22_HUMAN24-89661A:35-89 (gaps)60
1.3bENST000001608273bENSE00001592164chr16:29809695-29809822128KIF22_HUMAN89-132441A:89-13244
1.4ENST000001608274ENSE00001608077chr16:29809914-29810068155KIF22_HUMAN132-183521A:132-18352
1.5aENST000001608275aENSE00001623779chr16:29810296-29810505210KIF22_HUMAN184-253701A:184-253 (gaps)70
1.6ENST000001608276ENSE00001614981chr16:29810585-29810815231KIF22_HUMAN254-330771A:254-330 (gaps)77
1.7ENST000001608277ENSE00001784321chr16:29810949-29811102154KIF22_HUMAN331-382521A:331-607 (gaps)50
1.8ENST000001608278ENSE00001765213chr16:29811234-29811369136KIF22_HUMAN382-427460--
1.9ENST000001608279ENSE00001747434chr16:29814090-29814258169KIF22_HUMAN427-483570--
1.10ENST0000016082710ENSE00001597834chr16:29814770-29814929160KIF22_HUMAN484-537540--
1.11ENST0000016082711ENSE00001643614chr16:29815319-2981538668KIF22_HUMAN537-559230--
1.13ENST0000016082713ENSE00000868486chr16:29816135-29816347213KIF22_HUMAN560-630710--
1.14ENST0000016082714ENSE00000681418chr16:29816436-2981649560KIF22_HUMAN631-650200--
1.15ENST0000016082715ENSE00001318180chr16:29816584-29816706123KIF22_HUMAN651-665150--

(-) 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:290
 aligned with KIF22_HUMAN | Q14807 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:351
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379 
          KIF22_HUMAN    30 LSKIGATRRPPPARVRVAVRLRPFVDGTAGASDPPCVRGMDSCSLEIANWRNHQETLKYQFDAFYGERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTMLGSPEQPGVIPRALMDLLQLTREEGAEGRPWALSVTMSYLEIYQEKVLDLLDPASGDLVIREDCRGNILIPGLSQKPISSFADFERHFLPASRNRTVGATRLNQRSSRSHAVLLVKVDQRERLAPFRQREGKLYLIDLAGSEDNRRTGNKGLRLKESGAINTSLFVLGKVVDALNQGLPRVPYRDSKLTRLLQDSLGGSAHSILIANIAPERRFYLDTVSALNFAARSKEVINRPFTNESLQP 380
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----     ----3bfnA01 A:4                             4-369 Kinesin                                                                                                                                                                                                                                                                                  -- ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-----.....eeeeee....-----------------------------.eeeee..eee....hhhhhhhhhh..hhhhhh....eeeeee.....hhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeee...........ee.....ee......ee..hhhhhhhhhhhhh.-----------hhhhheeeeeeeeeeee......eeeeeeeeee......--------------...hhhhhhhhhhhhhhhh.....hhhhhhhhhhh........eeeeeeee..hhhhhhhhhhhhhhhh.eeeee-..-....... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------LL--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------SQ--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) -------------KINESIN_MOTOR_2  PDB: A:43-368 UniProt: 43-368                                                                                                                                                                                                                                                                                        ------------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO----------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:35-89 (gaps) UniProt: 24-89 [INCOMPLETE]   ------------------------------------------Exon 1.4  PDB: A:132-183 UniProt: 132-183           Exon 1.5a  PDB: A:184-253 (gaps) UniProt: 184-253                     Exon 1.6  PDB: A:254-330 (gaps) UniProt: 254-330                             Exon 1.7  PDB: A:331-607 (gaps) UniProt: 331-382   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.3b  PDB: A:89-132 UniProt: 89-132    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3bfn A  35 LYFQG-----PPARVRVAVRLRPFV-----------------------------ETLKYQFDAFYGERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTMLGSPEQPGVIPRALMDLLQLTREEGAEGRPWALSVTMSYLEIYQEKVLDLLDPASGDLVIREDCRGNILIPGLSQKPISSFADFERHFLPASR-----------RSSRSHAVLLVKVDQRERLAPFRQREGKLYLIDLAGSED--------------GAINTSLFVLGKVVDALNQGLPRVPYRDSKLTRLLQDSLGGSAHSILIANIAPERRFYLDTVSALNFAARSKEVI-xx-xxxxxxx 607
                                |    -|       49    |    -         -         -    |   89        99       109       119       129       139       149       159       169       179       189       199       209       219       229|        -  |    249       259       269       279|        -     | 299       309       319       329       339       349       359       369 || |||606|
                               39    40            54                            84                                                                                                                                               230         242                                   280            295                                                                       369 || ||||607-UNK
                                                                                                                                                                                                                                                                                                                                                                               501-UNK|||| 
                                                                                                                                                                                                                                                                                                                                                                                502-UNK||| 
                                                                                                                                                                                                                                                                                                                                                                                  601-UNK| 
                                                                                                                                                                                                                                                                                                                                                                                   602-UNK 
                                                                                                                                                                                                                                                                                                                                                                                    603-UNK
                                                                                                                                                                                                                                                                                                                                                                                     604-UNK
                                                                                                                                                                                                                                                                                                                                                                                      605-UNK
                                                                                                                                                                                                                                                                                                                                                                                       606-UNK

   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 3BFN)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BFN)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KIF22_HUMAN | Q14807)
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:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0051310    metaphase plate congression    The alignment of chromosomes at the metaphase plate (spindle equator), a plane halfway between the poles of the spindle.
    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:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    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:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    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.

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 Related Entries

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

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        KIF22_HUMAN | Q148072edu

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