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(-) Description

Title :  TUBULIN-DARPIN COMPLEX
 
Authors :  S. Ahmad, M. Knossow, B. Gigant
Date :  25 Nov 15  (Deposition) - 20 Jul 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,F
Keywords :  Darpin, Microtubule, Tubulin, Protein Binding, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahmad, L. Pecqueur, B. Dreier, D. Hamdane, M. Aumont-Nicaise, A. Pluckthun, M. Knossow, B. Gigant
Destabilizing An Interacting Motif Strengthens The Association Of A Designed Ankyrin Repeat Protein With Tubulin.
Sci Rep V. 6 28922 2016
PubMed-ID: 27380724  |  Reference-DOI: 10.1038/SREP28922

(-) 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)
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDST067
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: XL1BLUE
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric/Biological Unit (6, 15)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL8Ligand/IonGLYCEROL
3GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4LOC1Ligand/IonN-[(7S)-1,2,3,10-TETRAMETHOXY-9-OXO-6,7-DIHYDRO-5H-BENZO[D]HEPTALEN-7-YL]ETHANAMIDE
5MG1Ligand/IonMAGNESIUM ION
6SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ASP A:69 , ASP A:98 , ALA A:99 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , ILE A:171 , VAL A:177 , SER A:178 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , ILE A:231 , MG A:502 , HOH A:602 , HOH A:637 , HOH A:647 , HOH A:651 , HOH A:664 , HOH A:669 , LYS B:254binding site for residue GTP A 501
02AC2SOFTWAREGTP A:501 , HOH A:602 , HOH A:648 , HOH A:664 , HOH A:823binding site for residue MG A 502
03AC3SOFTWARELYS A:394 , GOL A:505 , HOH A:642 , HOH A:699 , HOH A:795 , ASN B:349binding site for residue SO4 A 503
04AC4SOFTWARESER A:178 , PRO A:222 , TYR A:224binding site for residue SO4 A 504
05AC5SOFTWARETYR A:172 , PRO A:173 , PRO A:175 , ARG A:390 , LYS A:394 , SO4 A:503 , HOH A:629 , HOH A:639 , HOH A:642binding site for residue GOL A 505
06AC6SOFTWAREHIS A:406 , GLU A:415 , HOH A:656binding site for residue GOL A 506
07AC7SOFTWAREGLN A:15 , ASN A:18 , THR A:225 , ASN A:228 , HOH A:705binding site for residue GOL A 507
08AC8SOFTWAREGLY 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 , PRO B:173 , VAL B:177 , ASP B:179 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228 , HOH B:607 , HOH B:611 , HOH B:641 , HOH B:647 , HOH B:653 , HOH B:748binding site for residue GDP B 501
09AC9SOFTWARETHR A:179 , ALA A:180 , VAL A:181 , HOH A:688 , CYS B:241 , LEU B:242 , LEU B:248 , ALA B:250 , LYS B:254 , LEU B:255 , ASN B:258 , VAL B:315 , ALA B:316 , ILE B:318 , ASN B:350 , LYS B:352 , ILE B:378 , HOH B:635 , HOH B:721binding site for residue LOC B 502
10AD1SOFTWARETHR B:223 , GLY B:225 , ARG B:278 , HOH B:784binding site for residue SO4 B 503
11AD2SOFTWAREASN B:54 , ARG B:88 , LYS B:124 , GLU B:125 , SER B:128 , HOH B:608 , HOH B:614 , HOH B:621binding site for residue GOL B 504
12AD3SOFTWAREPHE B:404 , LEU B:405 , HIS B:406 , TRP B:407 , HOH B:774 , HOH B:781 , ARG F:23 , TYR F:57 , GOL F:201 , HOH F:332binding site for residue GOL B 505
13AD4SOFTWAREARG B:401 , LYS B:402 , GOL B:505 , HOH B:734 , ARG F:23 , TYR F:57 , HOH F:319 , HOH F:321 , HOH F:332binding site for residue GOL F 201
14AD5SOFTWARETHR F:43 , ASP F:44 , ALA F:45binding site for residue GOL F 202
15AD6SOFTWAREHOH B:649 , ILE F:90 , GLY F:91 , HIS F:92 , HOH F:351 , HOH F:354binding site for residue GOL F 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EYP)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EYP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EYP)

(-) Exons   (0, 0)

(no "Exon" information available for 5EYP)

(-) 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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........eeeee.............hhhhhhhhhhhhhhh..........eeeeeeeeee..hhhhhhhhhhhhhhhh............eeeee................eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eyp A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV 437
                                    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        
                                                               37|                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                47                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhh.hhhh.eeee...eeee.eeeee..hhhhhhhhhh.hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhh...hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee........eeeeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eyp B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD 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     ||288       298       308       318       328       338       348       358 ||    376       386       396       406       416       426       436     
                                                                    42|                                                                                                                                                                                                                                      278|                                                                        360|                                                                        
                                                                     45                                                                                                                                                                                                                                       285                                                                         369                                                                        


Chain F from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eyp F  13 DLGKKLLEAARAGQDDEVRVLMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVSASDLMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLRLAAVMGHLKIVEALLKHGADVNAQ 142
                                    22        32        42        52        62        72        82        92       102       112       122       132       142
   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 5EYP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EYP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EYP)

(-) Gene Ontology  (8, 16)

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 ]  
 

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 Related Entries

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

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        D0VWY9_SHEEP | D0VWY9: 3hkb 3hkc 3hkd 3hke 3n2g 3n2k 3ryc 3ryf 3ryh 3ryi 3ut5 4drx 4eb6 4f61 4f6r 4hna 4lnu 4x1i 4x1k 4x1y 4x20 5kx5
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(-) Related Entries Specified in the PDB File

5eyl