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(-) Description

Title :  PSEUDO-ATOMIC MODEL OF DYNEIN MICROTUBULE BINDING DOMAIN-TUBULIN COMPLEX BASED ON A CRYOEM MAP
 
Authors :  S. Uchimura, T. Fujii, H. Takazaki, R. Ayukawa, Y. Nishikawa, I. Minour Y. Hachikubo, G. Kurisu, K. Sutoh, T. Kon, K. Namba, E. Muto
Date :  20 Mar 14  (Deposition) - 31 Dec 14  (Release) - 08 Apr 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  8.20
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Motor Protein-Cytoskeleton Complex, Motor Protein-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Uchimura, T. Fujii, H. Takazaki, R. Ayukawa, Y. Nishikawa, I. Minoura, Y. Hachikubo, G. Kurisu, K. Sutoh, T. Kon, K. Namba, E. Muto
A Flipped Ion Pair At The Dynein-Microtubule Interface Is Critical For Dynein Motility And Atpase Activation
J. Cell Biol. V. 208 211 2015
PubMed-ID: 25583999  |  Reference-DOI: 10.1083/JCB.201407039

(-) Compounds

Molecule 1 - DYNEIN HEAVY CHAIN, CYTOPLASMIC
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDB_G0276355, DHCA
    Organism Common: SLIME MOLD
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 44689
    Synonym: DYNEIN HEAVY CHAIN, CYTOSOLIC, DYHC
 
Molecule 2 - TUBULIN ALPHA-1A CHAIN
    Chains: A
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: ALPHA-TUBULIN 1, TUBULIN ALPHA-1 CHAIN
 
Molecule 3 - TUBULIN BETA CHAIN
    Chains: B
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: BETA-TUBULIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4TA11Ligand/IonTAXOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:11 , GLU A:71 , GTP A:502BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ALA A:99 , ALA A:100 , ASN A:101 , GLY A:142 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , THR A:179 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , MG A:501 , LEU B:248 , LYS B:254BINDING SITE FOR RESIDUE GTP A 502
3AC3SOFTWAREGLY 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 , ASP B:179 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228BINDING SITE FOR RESIDUE GDP B 501
4AC4SOFTWAREVAL B:23 , ASP B:26 , GLU B:27 , ASP B:226 , HIS B:229 , LEU B:230 , ALA B:233 , SER B:236 , PHE B:272 , LEU B:275 , THR B:276 , ARG B:278 , PRO B:360 , ARG B:369 , GLY B:370 , LEU B:371BINDING SITE FOR RESIDUE TA1 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J6P)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:412 -Met A:413
2Arg B:278 -Gly B:279
3His B:309 -Gly B:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J6P)

(-) Exons   (0, 0)

(no "Exon" information available for 3J6P)

(-) 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:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhhhhhhh..........eeee.hhhhhhhhhhh..........eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.......hhhhhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhh....eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeee..............hhhhhhhhhhhhhhh..........eeeeeeeee...hhhhhhhhhhhhhhhh...........eeeeee.................eeeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j6p A    2 RECISIHVGQAGVQIGNACWELYCLEHGIQPDGHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS  439
                                    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 ..eeeeeehhhhhhhhhhhhhhhhhhhh............hhhhhh...ee.......ee.eeeee.hhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.......hhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......ee...................hhhhhhhhhh..............eeeeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3j6p 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 D from PDB  Type:PROTEIN  Length:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........hhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                3j6p D 3382 TIKKKHLDEIKSLPKPPTPVKLAMEAVCLMLGGKKLEWADIRKKIMEPNFITSIINYDTKKMMTPKIREAITKGYLEDPGFDYETVNRASKACGPLVKWATAQTYYSE 3489
                                  3391      3401      3411      3421      3431      3441      3451      3461      3471      3481
   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 3J6P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J6P)

(-) Gene Ontology  (32, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg B:278 - Gly B:279   [ RasMol ]  
    Gly A:412 - Met A:413   [ RasMol ]  
    His B:309 - Gly B:310   [ RasMol ]  
 

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  3j6p
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 Related Entries

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

UniProtKB/Swiss-Prot
        DYHC_DICDI | P34036: 2gf8 3vkg 3vkh
        TBA1A_PIG | P02550: 1ffx 1ia0 1sa0 1sa1 1tub 1tvk 2hxf 2hxh 2p4n 2wbe 3j6e 3j6f 3j6g 3j6h 3j7i 4abo
        TBB_PIG | P02554: 1ffx 1ia0 1jff 1sa0 1sa1 1tub 1tvk 2hxf 2hxh 2wbe 3j6e 3j6f 3j6g 3j6h 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 3J6P)