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(-) Description

Title :  ATOMIC MODEL OF A MICROTUBULE SEAM BASED ON A CRYO-EM RECONSTRUCTION OF THE EB3-BOUND MICROTUBULE (MERGED DATASET CONTAINING TUBULIN BOUND TO GTPGAMMAS, GMPCPP, AND GDP)
 
Authors :  R. Zhang, E. Nogales
Date :  30 Jun 15  (Deposition) - 12 Aug 15  (Release) - 02 Sep 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Microtubule, Eb3, Seam, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, G. M. Alushin, A. Brown, E. Nogales
Mechanistic Origin Of Microtubule Dynamic Instability And Its Modulation By Eb Proteins.
Cell(Cambridge, Mass. ) V. 162 849 2015
PubMed-ID: 26234155  |  Reference-DOI: 10.1016/J.CELL.2015.07.012

(-) Compounds

Molecule 1 - TUBULIN ALPHA-1B CHAIN
    Chains: A, C
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: ALPHA-TUBULIN UBIQUITOUS, TUBULIN K-ALPHA-1, TUBULIN ALPHA- UBIQUITOUS CHAIN
 
Molecule 2 - TUBULIN BETA CHAIN
    Chains: B, D
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: BETA-TUBULIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GSP2Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , 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 , THR A:179 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , MG A:502 , LEU B:248 , LYS B:254BINDING SITE FOR RESIDUE GTP A 501
2AC2SOFTWAREGLU A:71 , GTP A:501 , LYS B:254BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREGLN B:11 , CYS B:12 , GLN B:15 , GLU B:71 , ALA B:99 , ASN B:101 , SER B:140 , GLY B:143 , GLY B:144 , THR B:145 , GLY B:146 , ASP B:179 , ASN B:206 , TYR B:224 , ASN B:228BINDING SITE FOR RESIDUE GSP B 501
4AC4SOFTWAREGLY C:10 , GLN C:11 , ALA C:12 , GLN C:15 , ALA C:99 , ASN C:101 , SER C:140 , GLY C:143 , GLY C:144 , THR C:145 , GLY C:146 , THR C:179 , GLU C:183 , ASN C:206 , TYR C:224 , ASN C:228 , MG C:502BINDING SITE FOR RESIDUE GTP C 501
5AC5SOFTWAREGLU C:71 , GTP C:501BINDING SITE FOR RESIDUE MG C 502
6AC6SOFTWAREGLU C:254 , GLY D:10 , GLN D:11 , CYS D:12 , GLU D:71 , SER D:140 , GLY D:143 , GLY D:144 , THR D:145 , GLY D:146 , ASP D:179 , ASN D:206 , ASN D:228BINDING SITE FOR RESIDUE GSP D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:273 -Pro A:274
2Ala B:273 -Pro B:274
3Ala C:273 -Pro C:274
4Ala D:273 -Pro D:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JAW)

(-) 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:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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.eeeeeehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeeee...hhhhhh....hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhh............eeeeee................eeeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jaw A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVE 441
                                    10        20        30      ||49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
                                                               37|                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                47                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhh............hhhhhhhhh.eeee...eeee.eeeee..hhhhhhhhhh.hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhh......eeeeeee.............hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee........eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jaw B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDAT 439
                                    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         
                                                                      44|                                                                                                                                                                                                                                                                                                                      360|                                                                      
                                                                       47                                                                                                                                                                                                                                                                                                                       369                                                                      


Chain C from PDB  Type:PROTEIN  Length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhhh........hhhhh.eeee...eeee.eeeee..hhhhhhhhhh......hhh.eee.......hhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhh........eeeee....hhhhhh...hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhh............eeeeee................eeeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jaw C   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVE 441
                                    10        20        30      ||49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
                                                               37|                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                47                                                                                                                                                                                                                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhh............hhhhhhhhh.eeee...eeee.eeeee..hhhhhhhhhh.hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhh......eeeeeee.............hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee........eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jaw D   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDAT 439
                                    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         
                                                                      44|                                                                                                                                                                                                                                                                                                                      360|                                                                      
                                                                       47                                                                                                                                                                                                                                                                                                                       369
   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 3JAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:273 - Pro A:274   [ RasMol ]  
    Ala B:273 - Pro B:274   [ RasMol ]  
    Ala C:273 - Pro C:274   [ RasMol ]  
    Ala D:273 - Pro D:274   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        TBA1B_PIG | Q2XVP4: 3j8x 3j8y 3jak 3jal 3jar 3jas 3jat 4zhq 4zi7 4zol 5ca0 5ezy 5fnv 5jqg 5kmg 5syc 5sye 5syf 5syg
        TBB_PIG | P02554: 1ffx 1ia0 1jff 1sa0 1sa1 1tub 1tvk 2hxf 2hxh 2wbe 3j6e 3j6f 3j6g 3j6h 3j6p 3j7i 3jak 3jal 3jar 3jas 3jat 4abo 4zhq 4zi7 4zol 5bmv 5fnv 5jqg 5kmg 5syc 5sye 5syf 5syg

(-) Related Entries Specified in the PDB File

3jak 3jal 3jar 3jas 3jat