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(-) Description

Title :  NUCLEOTIDE-FREE KINESIN MOTOR DOMAIN COMPLEXED WITH GMPCPP-MICROTUBULE
 
Authors :  M. Morikawa, H. Yajima, R. Nitta, S. Inoue, T. Ogura, C. Sato, N. Hirokaw
Date :  21 Feb 14  (Deposition) - 01 Apr 15  (Release) - 01 Apr 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  8.10
Chains :  Asym./Biol. Unit :  A,B,K
Keywords :  Kinesin, Motor Domain, Rigor-Conformation, Nucleotide-Free Kinesin, Microtubule, Gmpcpp-Microtubule, Tubulin, Axonal Transport, Structural Protein-Motor Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Morikawa, H. Yajima, R. Nitta, S. Inoue, T. Ogura, C. Sato, N. Hirokawa
X-Ray And Cryo-Em Structures Reveal Mutual Conformational Changes Of Kinesin And Gtp-State Microtubules Upon Binding
Embo J. 2015
PubMed-ID: 25777528  |  Reference-DOI: 10.15252/EMBJ.201490588

(-) Compounds

Molecule 1 - TUBULIN ALPHA-1A CHAIN
    Chains: A
    Fragment: UNP RESIDUES 2-437
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: ALPHA-TUBULIN 1, TUBULIN ALPHA-1 CHAIN
    Tissue: BRAIN
 
Molecule 2 - TUBULIN BETA CHAIN
    Chains: B
    Fragment: UNP RESIDUES 2-427
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: BETA-TUBULIN
    Tissue: BRAIN
 
Molecule 3 - KINESIN HEAVY CHAIN ISOFORM 5C
    Chains: K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-345
    Gene: KIF5C
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: KIF5C, KINESIN HEAVY CHAIN NEURON-SPECIFIC 2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1G2P1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:11 , GTP A:502BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLY A:142 , GLY A:143 , GLY A:144 , ALA A:174 , VAL A:177 , SER A:178 , THR A:179 , ALA A:180 , ASN A:206 , GLU A:207 , ILE A:209 , TYR A:210 , CYS A:213 , THR A:223 , TYR A:224 , ASN A:226 , LEU A:227 , MG A:501 , LEU B:248BINDING SITE FOR RESIDUE GTP A 502
3AC3SOFTWAREGLN B:11 , GLU B:71 , THR B:74 , G2P B:602BINDING SITE FOR RESIDUE MG B 601
4AC4SOFTWAREGLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , ASP B:69 , GLU B:71 , ALA B:99 , SER B:140 , GLY B:142 , GLY B:144 , THR B:145 , ASP B:179 , GLU B:183 , ASN B:206 , TYR B:224 , LEU B:227 , ASN B:228 , MG B:601BINDING SITE FOR RESIDUE G2P B 602
5AC5SOFTWARESER K:89 , SER K:90 , GLY K:91 , LYS K:92 , THR K:93BINDING SITE FOR RESIDUE SO4 K 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J6H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:384 -Ala A:385

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J6H)

(-) Exons   (0, 0)

(no "Exon" information available for 3J6H)

(-) 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:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhhhhhhhhhh............eeee.hhhhhhhhhhh..........eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhh.........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh........eee...............hhhhhhhhhhh.................eeeeeee..hhhhhhhhhhhhhh.............eeeee.................eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j6h A   2 RECISIHVGQAGVQIGNACWELYCLEHGIQPDGHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV 437
                                    11        21        31  ||    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
                                                           34|                                                                                                                                                                                                                                                                                                                                                                                        
                                                            61                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.eeee.hhhhhhhhhhhhhhhhh..................hhhhhh...........eeeee.hhhhhhhhh..hhhhh.hhh.eee...............hhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhh....eee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.........eeeee................hhhhhhhhh.........hhhhh.eeeeeeeee...hhhhhhhhhhhhhhhh............eeeee..........eeeeeee..hhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3j6h B   2 REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQD 437
                                    11        21        31        41  ||    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      |371       381       391       401       411       421       431      
                                                                     44|                                                                                                                                                                                                                                                                                                                      360|                                                                    
                                                                      47                                                                                                                                                                                                                                                                                                                       369                                                                    


Chain K from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...hhhhhhh.....eeee...eeee.....ee..eee....hhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhh.........hhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhhhhhhhhhh...............eeeeeeeeee......eeeeeeeeee.......hhhhhhhhhhhhhh..............hhhhh......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j6h K   5 AECSIKVMCRFRPLNEAEILRGDKFIPKFKGEETVVIGQGKPYVFDRVLPPNTTQEQVYNACAKQIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEKKSLSALGNVISALAEGTKTHVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAKTIKNT 330
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144||     185       195       205       215       225       235  ||   263       273       283       293       303       313       323       
                                                                                                                                                                      145|                                                          238|                                                                         
                                                                                                                                                                       177                                                           257
   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 3J6H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J6H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J6H)

(-) Gene Ontology  (23, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ile A:384 - Ala A:385   [ RasMol ]  
 

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  3j6h
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 Related Entries

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

UniProtKB/Swiss-Prot
        KIF5C_MOUSE | P28738: 1vfv 1vfw 1vfx 1vfz 2zfi 2zfj 2zfk 2zfl 2zfm 3wrd 3x2t
        TBA1A_PIG | P02550: 1ffx 1ia0 1sa0 1sa1 1tub 1tvk 2hxf 2hxh 2p4n 2wbe 3j6e 3j6f 3j6g 3j6p 3j7i 4abo
        TBB_PIG | P02554: 1ffx 1ia0 1jff 1sa0 1sa1 1tub 1tvk 2hxf 2hxh 2wbe 3j6e 3j6f 3j6g 3j6p 3j7i 3jak 3jal 3jar 3jas 3jat 3jaw 4abo 4zhq 4zi7 4zol 5bmv 5fnv 5jqg 5kmg 5syc 5sye 5syf 5syg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3J6H)