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(-) Description

Title :  STRUCTURE OF THE COMPLEX OF A MITOTIC KINESIN WITH ITS CALCIUM BINDING REGULATOR
 
Authors :  M. V. Vinogradova
Date :  20 Apr 09  (Deposition) - 19 May 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,E
Keywords :  Kinesin, Motor Protein, Regulation, Complex, Calcium, Ef- Hand, Calmodulin, Atp-Binding, Microtubule, Nucleotide- Binding, Motor Protein/Calcium Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. V. Vinogradova, G. G. Malanina, A. S. Reddy, R. J. Fletterick
Structure Of The Complex Of A Mitotic Kinesin With Its Calcium Binding Regulator.
Proc. Natl. Acad. Sci. Usa V. 106 8175 2009
PubMed-ID: 19416847  |  Reference-DOI: 10.1073/PNAS.0811131106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KINESIN-LIKE CALMODULIN-BINDING PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 875-1260
    GeneAT5G65930
    MutationYES
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
 
Molecule 2 - KCBP INTERACTING CA2+-BINDING PROTEIN
    ChainsE
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneKIC
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA1Ligand/IonCALCIUM ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , HOH A:25 , HOH A:84 , HOH A:85 , HOH A:89 , HOH A:93 , HOH A:99 , MG A:601 , ARG A:897 , PRO A:898 , GLN A:971 , GLY A:973 , SER A:974 , GLY A:975 , LYS A:976 , THR A:977 , PHE A:978BINDING SITE FOR RESIDUE ADP A 600
2AC2SOFTWAREHOH A:84 , HOH A:85 , HOH A:86 , HOH A:87 , ADP A:600 , THR A:977BINDING SITE FOR RESIDUE MG A 601
3AC3SOFTWAREVAL A:964 , LYS A:1111 , SER A:1113 , SER A:1174BINDING SITE FOR RESIDUE MG A 602
4AC4SOFTWAREASP E:87 , ASP E:89 , ASP E:91 , ALA E:93 , GLU E:98 , HOH E:147BINDING SITE FOR RESIDUE CA E 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H4S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H4S)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.KIC_ARATH74-109  1E:74-109
2EF_HAND_1PS00018 EF-hand calcium-binding domain.KIC_ARATH87-99  1E:87-99
3KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KN14E_ARATH888-1209  1A:889-1210
4KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KN14E_ARATH1109-1120  1A:1110-1121

(-) Exons   (0, 0)

(no "Exon" information available for 3H4S)

(-) 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:359
 aligned with KN14E_ARATH | Q9FHN8 from UniProtKB/Swiss-Prot  Length:1260

    Alignment length:376
                                   888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      
         KN14E_ARATH    879 YNTIEDMKGKIRVYCRIRPLNEKESSEREKQMLTTVDEFTVEHPWKDDKRKQHIYDRVFDMRASQDDIFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTIYGHESNPGLTPRATKELFNILKRDSKRFSFSLKAYMVELYQDTLVDLLLPKSARRLKLEIKKDSKGMVFVENVTTIPISTLEELRMILERGSERRHVSGTNMNEESSRSHLILSVVIESIDLQTQSAARGKLSFVDLAGSERVKKSGSAGCQLKEAQSINKSLSALGDVIGALSSGNQHIPYRNHKLTMLMSDSLGGNAKTLMFVNVSPAESNLDETYNSLLYASRVRTIVNDPSKHISSKEMVRLKKLVAYWKEQAGKKGEEEDLVDIEEDRTR 1254
               SCOP domains -     d3h4sa1 A:886-1255 automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----...eeeeeeee...hhhhhhh......eeee..eeee.......eeee..eee....hhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhee..eehhhhhhhhhhhhhhhhh...eeeeeeeeeeeee..eeee.....---....eeee.....eeee....eee.hhhhhhhhhhhhhh.---------hhhhhheeeeeeeeeeee.....eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------KINESIN_MOTOR_2  PDB: A:889-1210 UniProt: 888-1209                                                                                                                                                                                                                                                                                --------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO-------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3h4s A  880 Y-----MKGKIRVYCRIRPLNEKESSEREKQMLTTVDEFTVEHPWKDDKRKQHIYDRVFDMRASQDDIFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTIYGHESNPGLTPRATKELFNILKRDSKRFSFSLKAYMVELYQDTLVDLLLPK---RLKLEIKKDSKGMVFVENVTTIPISTLEELRMILERGSER---------EESSRSHLILSVVIESIDLQTQSAARGKLSFVDLAGSERVKKSGSAGNQLKEAQSINKSLSALGDVIGALSSGNQHIPYRNHKLTMLMSDSLGGNAKTLMFVNVSPAESNLDETYNSLLYASRVRTIVNDPSKHISSKEMVRLKKLVAYWKEQAGKKGEEEDLVDIEEDRTR 1255
                            |     |889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029 |   |1039      1049      1059      1069    |    -    | 1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      
                          880   886                                                                                                                                             1031   |                                   1074      1084                                                                                                                                                                           
                                                                                                                                                                                    1035                                                                                                                                                                                                                            

Chain E from PDB  Type:PROTEIN  Length:96
 aligned with KIC_ARATH | Q9ZPX9 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:107
                                    28        38        48        58        68        78        88        98       108       118       
           KIC_ARATH     19 ETKYEDMLPVMAEKMDVEEFVSELCKGFSLLADPERHLITAESLRRNSGILGIEGMSKEDAQGMVREGDLDGDGALNQTEFCVLMVRLSPEMMEDAETWLEKALTQE  125
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----------hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------EF_HAND_2  PDB: E:74-109            ---------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------EF_HAND_1    -------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                3h4s E   19 ETKY-----------DVEEFVSELCKGFSLLADPERHLITAESLRRNSGILGIEGMSKEDAQGMVREGDLDGDGALNQTEFCVLMVRLSPEMMEDAETWLEKALTQE  125
                               |     -     |  38        48        58        68        78        88        98       108       118       
                              22          34                                                                                           

   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  (0, 0)

(no "CATH Domain" information available for 3H4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H4S)

(-) Gene Ontology  (17, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KN14E_ARATH | Q9FHN8)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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: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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0010091    trichome branching    Any process involved in the formation of branches in plant hair cells. An example of this process is found in Arabidopsis thaliana.
cellular component
    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.

Chain E   (KIC_ARATH | Q9ZPX9)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0010091    trichome branching    Any process involved in the formation of branches in plant hair cells. An example of this process is found in Arabidopsis thaliana.

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 Related Entries

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        KN14E_ARATH | Q9FHN84frz

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