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(-) Description

Title :  KINESIN MOTOR DOMAIN IN THE ADP-MG-ALFX STATE IN COMPLEX WITH TUBULIN AND A DARPIN
 
Authors :  B. Gigant, M. Knossow
Date :  19 Oct 12  (Deposition) - 12 Jun 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym./Biol. Unit :  A,B,D,K
Keywords :  Alpha-Tubulin, Beta-Tubulin, Darpin, Gtpase, Kinesin, Microtubule, Tubulin, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gigant, W. Wang, B. Dreier, Q. Jiang, L. Pecqueur, A. Pluckthun, C. Wang, M. Knossow
Structure Of A Kinesin-Tubulin Complex And Implications For Kinesin Motility.
Nat. Struct. Mol. Biol. V. 20 1001 2013
PubMed-ID: 23872990  |  Reference-DOI: 10.1038/NSMB.2624

(-) Compounds

Molecule 1 - TUBULIN ALPHA CHAIN
    Chains: A
    Organ: BRAIN
    Organism Common: DOMESTIC SHEEP,LAMBS,WILD SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
    Other Details: BRAIN
 
Molecule 2 - TUBULIN BETA CHAIN
    Chains: B
    Organ: BRAIN
    Organism Common: DOMESTIC SHEEP,LAMBS,WILD SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
    Other Details: BRAIN
 
Molecule 3 - DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDST067 (PQE30 DERIVATIVE)
    Expression System Strain: XL1BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630
 
Molecule 4 - KINESIN-1 HEAVY CHAIN
    Chains: K
    Engineered: YES
    Expression System: ESCHERICHIA
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 561
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-349
    Gene: KIF5B, KNS, KNS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CONVENTIONAL KINESIN HEAVY CHAIN, UBIQUITOUS KINESIN HEAVY CHAIN, UKHC

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF2Ligand/IonTETRAFLUOROALUMINATE ION
3GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
5MG3Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ASP A:69 , ASP A:98 , ALA A:99 , ALA A:100 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , VAL A:177 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , ILE A:231 , MG A:601 , LYS B:254BINDING SITE FOR RESIDUE GTP A 600
2AC2SOFTWAREGTP A:600BINDING SITE FOR RESIDUE MG A 601
3AC3SOFTWAREGLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , SER B:140 , GLY B:143 , GLY B:144 , THR B:145 , GLY B:146 , VAL B:177 , SER B:178 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228 , MG B:502 , ALF B:503BINDING SITE FOR RESIDUE GDP B 501
4AC4SOFTWAREGLN B:11 , GLU B:71 , GDP B:501 , ALF B:503BINDING SITE FOR RESIDUE MG B 502
5AC5SOFTWAREGLU B:71 , ALA B:99 , GLY B:100 , ASN B:101 , GLY B:144 , THR B:145 , GDP B:501 , MG B:502BINDING SITE FOR RESIDUE ALF B 503
6AC6SOFTWARELYS D:101 , ARG K:14 , ARG K:16 , PRO K:17 , SER K:88 , SER K:89 , GLY K:90 , LYS K:91 , THR K:92 , HIS K:93 , ASN K:198 , MG K:402 , ALF K:403 , HOH K:501 , HOH K:502BINDING SITE FOR RESIDUE ADP K 401
7AC7SOFTWARETHR K:92 , SER K:202 , ADP K:401 , ALF K:403 , HOH K:501 , HOH K:502BINDING SITE FOR RESIDUE MG K 402
8AC8SOFTWARETHR K:87 , SER K:88 , LYS K:91 , ASN K:198 , SER K:201 , SER K:202 , ALA K:233 , GLY K:234 , ADP K:401 , MG K:402 , HOH K:501 , HOH K:502BINDING SITE FOR RESIDUE ALF K 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HNA)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:273 -Pro A:274
2Ala B:273 -Pro B:274
3Gln B:281 -Gln B:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HNA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HNA)

(-) Exons   (0, 0)

(no "Exon" information available for 4HNA)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hnaa1 A:1-245 automated matches                                                                                                                                                                                                             d4hnaa2 A:246-437 automated matches                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhh.eee.....eee.eeeee..hhhhhhhhhh......hhh.eee.......hhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeeee.............hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhh.............eeeee................eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hna A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV 437
                                    10        20        30       |47        57        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
                                                                38|                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                 46                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4hnab1 B:1-245 automated matches                                                                                                                                                                                                                  d4hnab2 B:246-441 automated matches                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhh............hhhhhhhhh.eee.....eee.eeeee..hhhhhhhhhh.hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......eeeeeee.............hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee........eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hna B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD 441
                                    10        20        30        40   ||   52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       370       380       390       400       410       420       430       440 
                                                                      44|                                                                                                                                                                                                                                                                                                                      360|                                                                        
                                                                       47                                                                                                                                                                                                                                                                                                                       369                                                                        


Chain D from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4hnad_ D: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hna D  11 GSDLGKKLLEAARAGQDDEVRILMANGADVNAEDDSGKTPLHLAAIKGHLEIVEVLLKHGADVNAADKMGDTPLHLAALYGHLEIVEVLLKNGADVNATDTYGFTPLHLAADAGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN 169
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain K from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4hnak_ K: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...hhhhhh.......eee...eeee..eeee...ee....hhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhh.........hhhhhhhhhhhhhhhhh...eeeeeeeeeeeee..eeee.........eeee.....eeee....eee.hhhhhhhhhhhhhh...ee.......ee..eeeeeeeeeeee.....eeeeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hna K   5 AESNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDAAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGATERFVSSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNARTTIVICCSPSSYNESETKSTLLFGQRAKTIKNTVSVNVELTA 337
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   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  (4, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HNA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HNA)

(-) Gene Ontology  (33, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:273 - Pro A:274   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        KINH_HUMAN | P33176: 1bg2 1mkj 2p4n 3j8x 3j8y 4lnu 5lt0 5lt1 5lt2 5lt3 5lt4
UniProtKB/TrEMBL
        D0VWY9_SHEEP | D0VWY9: 3hkb 3hkc 3hkd 3hke 3n2g 3n2k 3ryc 3ryf 3ryh 3ryi 3ut5 4drx 4eb6 4f61 4f6r 4lnu 4x1i 4x1k 4x1y 4x20 5eyp 5kx5
        D0VWZ0_SHEEP | D0VWZ0: 3hkb 3hkc 3hkd 3hke 3n2g 3n2k 3ryc 3ryf 3ryh 3ryi 3ut5 4drx 4eb6 4f61 4f6r 4x1i 4x1k 4x1y 4x20 5eyp 5kx5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HNA)