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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF HUMAN KINESIN-8 MOTOR DOMAIN
 
Authors :  K. Brejc, C. A. Moores, J. Hartman
Date :  11 Feb 10  (Deposition) - 10 Nov 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Motor Protein, Nucleotide Binding, Microtubule Binding, Atp-Binding, Cell Projection, Cytoskeleton, Glycoprotein, Microtubule, Nucleotide-Binding, Nucleus, Phosphoprotein, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Peters, K. Brejc, L. Belmont, A. J. Bodey, Y. Lee, M. Yu, J. Guo, R. Sakowicz, J. Hartman, C. A. Moores
Insight Into The Molecular Mechanism Of The Multitasking Kinesin-8 Motor.
Embo J. V. 29 3437 2010
PubMed-ID: 20818331  |  Reference-DOI: 10.1038/EMBOJ.2010.220

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KIF18A
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-355
    GeneKIF18A, OK/SW-CL.108
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMARROW STROMAL KIF18A, MS-KIF18A

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:120 , HOH A:446 , HOH A:450 , HOH A:457 , ADP A:500BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREARG A:19 , PRO A:20 , ALA A:114 , THR A:115 , GLY A:116 , ALA A:117 , GLY A:118 , LYS A:119 , THR A:120 , HIS A:121 , HOH A:372 , HOH A:376 , HOH A:383 , HOH A:397 , HOH A:446 , HOH A:450 , MG A:501BINDING SITE FOR RESIDUE ADP A 500
3AC3SOFTWARETHR B:120 , HOH B:382 , HOH B:399 , HOH B:484 , HOH B:494 , ADP B:500BINDING SITE FOR RESIDUE MG B 501
4AC4SOFTWAREARG B:17 , ARG B:19 , PRO B:20 , ALA B:114 , THR B:115 , GLY B:116 , ALA B:117 , GLY B:118 , LYS B:119 , THR B:120 , HIS B:121 , HOH B:360 , HOH B:376 , HOH B:382 , HOH B:388 , HOH B:390 , HOH B:408 , HOH B:443 , HOH B:461 , HOH B:481 , HOH B:484 , HOH B:494 , MG B:501BINDING SITE FOR RESIDUE ADP B 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LRE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049702P334SKI18A_HUMANPolymorphism34913484A/BP334S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049702P334SKI18A_HUMANPolymorphism34913484AP334S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049702P334SKI18A_HUMANPolymorphism34913484BP334S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049702P334SKI18A_HUMANPolymorphism34913484A/BP334S

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

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KI18A_HUMAN11-355  1B:11-355
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KI18A_HUMAN252-263
 
  2A:252-263
B:252-263
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KI18A_HUMAN11-355  0-
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KI18A_HUMAN252-263
 
  1A:252-263
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KI18A_HUMAN11-355  1B:11-355
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KI18A_HUMAN252-263
 
  1-
B:252-263
Biological Unit 3 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KI18A_HUMAN11-355  1B:11-355
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KI18A_HUMAN252-263
 
  2A:252-263
B:252-263

(-) Exons   (0, 0)

(no "Exon" information available for 3LRE)

(-) Sequences/Alignments

Asymmetric 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 KI18A_HUMAN | Q8NI77 from UniProtKB/Swiss-Prot  Length:898

    Alignment length:342
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351  
          KI18A_HUMAN    12 MKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGKKTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPLAVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLRQQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALADSKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAK 353
               SCOP domains d3lrea_ A: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhh.....eee....eeee.-----------------------...eeee..eee....hhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhh......hhhhhhhhhhhhhhhhh...eeeeeeeeeeeee..eeee........eeee.....eeee........hhhhhhhhhhhhhhh....-----......eeeeeeeeeeee...........eeeeeee......-----------------hhhhhhhhhhhhhhh--------.hhhhhhhhhhh........eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------- SAPs(SNPs)
                PROSITE (1) KINESIN_MOTOR_2  PDB: - UniProt: 11-355                                                                                                                                                                                                                                                                                                                PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lre A  12 MKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFD-----------------------NKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPLAVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQH-----ATSSRSHAVFQIYLRQQDKTASINQNVRIAKMSLIDLAGSER-----------------NRSLLALGNVINALA--------IPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAK 353
                                    21        31        41   |     -         -       |71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     |   - |     231       241       251       261  |      -         -|      291    |    -   |   311       321       331       341       351  
                                                            45                      69                                                                                                                                                 217   223                                      264               282           296      305                                                

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with KI18A_HUMAN | Q8NI77 from UniProtKB/Swiss-Prot  Length:898

    Alignment length:346
                                    19        29        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      
          KI18A_HUMAN    10 HHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGKKTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPLAVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLRQQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALADSKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDI 355
               SCOP domains d3lreb_ B: automated matches                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Kinesin-3lreB01 B:17-355                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) -------Kinesin-3lreB02 B:17-355                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author ...eeeeee...hhhhhh......eee....eeee.----------------------....eeee..eee....hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhh......hhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeee..........-----..............hhhhhhhhhhhhhhh..............eeeeeeeeeeeee.........eeeeeeeee.......-------------...hhhhhhhhhhhhhhhhh.------hhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S--------------------- SAPs(SNPs)
                PROSITE (1) -KINESIN_MOTOR_2  PDB: B:11-355 UniProt: 11-355                                                                                                                                                                                                                                                                                                            PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO-------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lre B  10 HHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFD----------------------QNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPLAV-----KGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLRQQDKTASINQNVRIAKMSLIDLAGSERA-------------TNINRSLLALGNVINALADSK------PYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDI 355
                                    19        29        39     |   -         -        69        79        89        99       109       119       129       139       149       159       169       179     | 189       199       209       219       229       239       249       259     |   -       279       289       299      |309       319       329       339       349      
                                                              45                     68                                                                                                            179   185                                                                             265           279                 299    306                                                 

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LRE)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KI18A_HUMAN | Q8NI77)
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:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    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:0070463    tubulin-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of a tubulin dimer to accelerate release of ADP and phosphate.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    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:0007140    male meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
    GO:0007019    microtubule depolymerization    The removal of tubulin heterodimers from one or both ends of a microtubule.
    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:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0070507    regulation of microtubule cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    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:0072520    seminiferous tubule development    The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    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:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005828    kinetochore microtubule    Any of the spindle microtubules that attach to the kinetochores of chromosomes by their plus ends, and maneuver the chromosomes during mitotic or meiotic chromosome segregation.
    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:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    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:1990023    mitotic spindle midzone    The area in the center of the anaphase spindle consisting of microtubules, microtubule bundling factors and kinesin motors where the spindle microtubules from opposite poles overlap in an antiparallel manner.
    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:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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