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(-) Description

Title :  NUCLEOTIDE-FREE KINESIN MOTOR DOMAIN IN COMPLEX WITH TUBULIN AND A DARPIN
 
Authors :  L. Cao, B. Gigant, M. Knossow
Date :  12 Jul 13  (Deposition) - 03 Dec 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A,B,D,K
Keywords :  Alpha-Tubulin, Apo-Kinesin, Beta-Tubulin, Darpin, Kinesin, Microtubule, Tubulin, Cell Cycle-Motor Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Cao, W. Wang, Q. Jiang, C. Wang, M. Knossow, B. Gigant
The Structure Of Apo-Kinesin Bound To Tubulin Links The Nucleotide Cycle To Movement
Nat Commun V. 5 5364 2014
PubMed-ID: 25395082  |  Reference-DOI: 10.1038/NCOMMS6364

(-) Compounds

Molecule 1 - TUBULIN ALPHA CHAIN
    Chains: A
    Organ: BRAIN
    Organism Common: SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
 
Molecule 2 - TUBULIN BETA CHAIN
    Chains: B
    Organ: BRAIN
    Organism Common: SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
 
Molecule 3 - DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1
    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 COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-325
    Gene: KIF5B
    Mutation: YES
    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  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5MG1Ligand/IonMAGNESIUM ION
6SO411Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ASP A:98 , ALA A:99 , 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:502 , HOH A:601 , HOH A:603 , HOH A:621 , HOH A:627 , HOH A:629 , HOH A:636 , HOH A:664 , HOH A:810 , LYS B:254BINDING SITE FOR RESIDUE GTP A 501
02AC2SOFTWAREGTP A:501 , HOH A:601 , HOH A:602 , HOH A:627 , HOH A:636BINDING SITE FOR RESIDUE MG A 502
03AC3SOFTWAREVAL A:177 , ARG A:221 , TYR A:224 , HOH A:645 , HOH A:825BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREPRO A:175 , LYS A:394 , HOH A:858 , ASN B:349BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWAREARG A:79 , PRO A:89 , LEU A:92 , HOH A:651 , HOH A:652 , HOH A:718 , HOH A:721 , PHE D:150 , LEU D:165 , GLN D:166 , HOH D:305BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWAREGLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , SER B:140 , GLY B:142 , GLY B:143 , GLY B:144 , THR B:145 , GLY B:146 , SER B:178 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228 , HOH B:601 , HOH B:604 , HOH B:606 , HOH B:632 , HOH B:666 , HOH B:672 , HOH B:798 , HOH B:813BINDING SITE FOR RESIDUE GDP B 501
07AC7SOFTWAREHOH A:605 , ARG B:158 , PRO B:162 , ASP B:163 , ARG B:164 , ASN B:197 , ASP B:199 , ARG B:253 , HOH B:633BINDING SITE FOR RESIDUE MES B 502
08AC8SOFTWAREPHE B:296 , TYR B:312 , ASN B:339 , TYR B:342 , PHE B:343 , SO4 B:509BINDING SITE FOR RESIDUE GOL B 503
09AC9SOFTWAREASN B:54 , ARG B:88 , LYS B:124 , GLU B:125 , SER B:128BINDING SITE FOR RESIDUE GOL B 504
10BC1SOFTWAREHIS B:192 , GLN B:193 , GLU B:196 , ASN B:197BINDING SITE FOR RESIDUE SO4 B 505
11BC2SOFTWARETHR B:223 , GLY B:225 , ARG B:278 , HOH B:816BINDING SITE FOR RESIDUE SO4 B 506
12BC3SOFTWAREARG B:400 , HOH B:741 , HOH B:772 , TRP D:112BINDING SITE FOR RESIDUE SO4 B 507
13BC4SOFTWAREHIS B:107 , TYR B:108 , GLN B:193 , HOH B:779 , HOH B:812BINDING SITE FOR RESIDUE SO4 B 508
14BC5SOFTWAREPHE B:296 , ASP B:297 , SER B:298 , ASP B:306 , ARG B:308 , GOL B:503BINDING SITE FOR RESIDUE SO4 B 509
15BC6SOFTWAREGLY B:100 , ASN B:102 , LYS B:105 , TRP B:407 , HOH B:786BINDING SITE FOR RESIDUE SO4 B 510
16BC7SOFTWARELYS B:402 , ARG D:23 , TYR D:57 , HOH D:333 , HOH D:383 , HOH D:387BINDING SITE FOR RESIDUE GOL D 201
17BC8SOFTWAREHIS A:406 , LYS K:256 , SER K:259 , ASN K:263 , ASP K:279 , HOH K:526 , HOH K:528BINDING SITE FOR RESIDUE GOL K 401
18BC9SOFTWARESER K:88 , SER K:89 , GLY K:90 , LYS K:91 , THR K:92BINDING SITE FOR RESIDUE SO4 K 402
19CC1SOFTWAREGLU B:196 , ARG K:278 , SER K:280 , LYS K:281 , HOH K:543BINDING SITE FOR RESIDUE SO4 K 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Met A:1 -Arg A:2
2Ala A:273 -Pro A:274
3Ala A:281 -Tyr A:282
4Ala B:273 -Pro B:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LNU)

(-) 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:434
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhhh..............hhhhh.eee.....eee.eeeee..hhhhhhhhhh......hhh.eee.......hhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeeee.............hhhhhhhhhhhhhhh..........eeeeeeeeee..hhhhhhhhhhhhhhhh............eeeee................eeeeeeeee..hhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lnu A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV 437
                                    10        20        30        40||      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       363       373       383       393       403       413       423       433    
                                                                   41|                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                    45                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhh.hhhh.eeee...eeee.eeeee...hhhhhhhhh.hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......eeeeeee.............hhhhhhhhhhhhhhh....hhhhh.eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lnu B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSIHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lnu D  13 DLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN 169
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       


Chain K from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh.......eee...eee.........eee....hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhh..........hhhhhhhhhhhhh......eeeeeeeeeeeee..eeee.........eeee.....eeee....ee..hhhhhhhhhhhhhh.........eeeeeeeeeeee.....eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lnu K   8 NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDAAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGATERFVSSPDEVMDTIDEGKSNRHVASSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNARTTIVICCSPSSYNESETKSTLLFGQRAK 323
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     ||204       214       224       234       244       254       264       274       284       294       304       314         
                                                                                                                                                                                                                   193|                                                                                                                          
                                                                                                                                                                                                                    201
   Legend:   → Mismatch (orange background)
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  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 4LNU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4hna 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 4hna 4x1i 4x1k 4x1y 4x20 5eyp 5kx5

(-) Related Entries Specified in the PDB File

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