Structure of the vertebrate gamma-Tubulin Ring Complex

2024-05-22 REL PDBe PDBe PDBe 2019-11-13 2019-12-11 2019-12-11 2024-05-22 Structure of the vertebrate gamma-Tubulin Ring Complex Zupa E Pfeffer S gamma-Tubulin Ring Complex, microtubule nucleation, CELL CYCLE Liu P Zupa E Neuner A Bohler A Loerke J Flemming D Ruppert T Rudack T Peter C Spahn C Gruss OJ Pfeffer S Schiebel E Insights into the assembly and activation of the microtubule nucleator gamma-TuRC. Nature UK 578 467 471 2020 31856152 doi:10.1038/s41586-019-1896-6 1476-4687 0006 NATUAS 6tf9 FULLOVERLAP Vertebrate gamma-Tubulin Ring Complex Vertebrate gamma-Tubulin Ring Complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Xenopus laevis 2.2 Helix 1 Xenopus laevis 0.0020792719999999996 1 LEVO AAAAAAAAAAAAAAAAAAAAAAAAAAAAA Belt helices 1,2,3,4 Xenopus laevis 0.000942027 4 LEVO AAAAAAAAAAAAA Belt helix 5 Xenopus laevis 0.002221427 1 LEVO AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Belt helix 6 Xenopus laevis 0.001652805 1 LEVO AAAAAAAAAAAAAAAAAAAAAAA Belt helix 7 Xenopus laevis 0.0012974159999999998 1 LEVO AAAAAAAAAAAAAAAAAA Belt helices 8,9,10 Xenopus laevis 0.001084182 3 LEVO AAAAAAAAAAAAAAA Belt helices 11,12 Xenopus laevis 0.001013105 2 LEVO AAAAAAAAAAAAAA Belt helices 13,14,15 and Helix 2 Xenopus laevis 0.00115526 4 LEVO AAAAAAAAAAAAAAAA Belt helix 16 Xenopus laevis 0.001226338 1 LEVO AAAAAAAAAAAAAAAAA Gamma-tubulin complex component 3 homolog Xenopus laevis 0.10378935199999999 5 LEVO MAVPDQKSPNVLLQNLCCRILGKGEADVAQQFQYAVRVIGSNFAPTVERDEFLVTEKIKKEFVRQRREADGALFSELHRK LQSQGVLKNRWSILYLLLSLSEDPRKQPNKTSSFAALFAQALPRDAHSTPYYYARPQSLPLSYQDRNVQCAQNAASIGSS GISSIGMYALNGPTPQSIIQGQSNQTPNMGDALRQQLGSRLAWTLAAGQQPSQQSTTTKGLPNTVSRNVPRTRREGDSSG SVEITETSLVRDLLYVFQGIDGKFVKMCNSENCYKVDGKVAVSKSLKDITSKLSELGWLHNKIKKYTDQRSLDRAFGLVG QSFCAALHQELKEYYRLLSVLHSQLQVEDDQGVNLGVESSLTLRRLLVWTFDPKIRLKTLAALVDHCQGRKGGELASAVH AYTKTGDPYMRSLVQHILGLVAYPILNFLYRWIYDGELEDTYHEFFVASDPVVKTDRLWHDKYSLRKSMIPSFMTMDQSR KVLLIGKSINFLHQVCHDQTPASKAMAVGKSAESPKDAAELFTDLENAFQTKIDAAYFDTSKYLLDVLNKNYNLLEHMQA MRRYLLLGQGDFIRHLMDLLKPELVRPATTLYQHNLTGILETAVRATNAQFDNPEILKRLDVRLLEVSPGDTGWDVFSLD YHVDGPIATVFTRECMSHYLRVFNFLWRAKRMEYILTDIWKGHMCNAKLLKGMPELSGVLHQCHILASEMVHFIHQMQYY ITFEVLECSWDELWNKVLKAQDLDHIIAAHDVFLDTIISRCLLDSESRALLNQLRAVFDQIIEFQNAQDALYRAALEELQ QRLQFEERKKERESEGEWGVTAAEEDVENKRIQEFQESIPKMRSQLRILTHFYQGIVQQFLVLLTTSTDESLRFLSFRLD FNEHYKAREPRLRVSMGTRGRRSFHV O73787 Gamma-tubulin complex component 2 Xenopus laevis 0.103468312 5 LEVO MSEFRIHHDVNELISLLHVFGLEGADVYIDLLQKNRTPYVTTSVSTHSAKVKIAEFSRTPDDFLKKYEELKSKNTRNLDP LVYLLSKLIEDKETLQYLQQNAKDKAELATSSVTSVSLPIAPNTSKISMQELEELRRQLETATVAVSCSHQPVEVLRKFL RDKLNKKHTGHPVPVFPSWVYERPALTGDFMSFSNPSTDVTVSIGTLPLPSQETCLVEDLLYILIGVDGRYISVQPLVGR QSRSFSVEQNLDSSVKELVNRILPVATNYSTVTRFVEENSSFEYGQVNHALGAAMRTLGKEYMILISQLEHLQRQGLLSL QKLWFYIQPTLRTMEVLASIATSLNKGECFGGATLSLLHDRTFGYTGDSQAQELCLYLTKAASAPYFDILERWIYRGIIN DPYSEFMVEEHELQKEKIQEDYNDKYWDQRYTIVQQQIPSFLQKVADKILSTGKYLNVVRECGHDVTCPDAKEITYTLKE QAYVERIEKAYNYASKVLLDFLMEEEELVAHLRSIKHYFLMDQGDFFVHFMDLTEEELKKPVDDIIPTRLEALLELALRM STANTDPFKDDLKIELMPHDLITQLLRVLAIETHQEKALINSDPTELALSGLESFSFDYIVKWPLSLIINRKALTRYQML FRHMFYCKHVERLLCNVWISNKTAKQFSLHSAKWFAGAFTLRQRMLNFVQNIQYYMMFEVMEPTWHILEKNLKSASNIDD VLSHHTSFLDNCLKDCMLTNPELLKIFSKLMSVCVMFTNCLQRFTQSMQVQTEMEHLTLEHGTMMGPPTQCERTEEALKK KLTSKYLEEHIDKFPSSFGFESTINNFDSNFSAHLMDLLDKLSMYSTSDCEHSMINIIYRLDFNGFYTERLKQLSSERNQ KSAPLLGPAQHAVSTK Gamma tubulin ring protein Xenopus laevis 0.184506188 1 LEVO MLSFNLRICGMSSEADRLEELVEYLEQSNGIQISDLHAVLELLVELSGTGPPQLLPPKRDYFKNNKYVGRNVKYQGYDYY DVQVFEADLGTTVAYQELEISTTIQRTLQIMEAAPGTGLPALSFFSQNDLSSDKFEKETRGSLFGALVHSRTNDMDIKLD MPPVPENADLSGLAIKVPQSIDQSEDEGFQSASNMTPDSQSEPSMTPDIDVWEAVLTYGPSKRRCWERIGCPPGKREEPY VTEAGREAFDKLYKLHEGGLQILSATTLQPQLVLLEETDLVKAVLNVLIGVVSSTFSYNQALQSFAVKQGVYISGTSPDN VSSLLTQVAEYGTYYTRLSHFSLLTVLDSSHSNGLVFQAFTSGLRKYLQYYRACVLSTPASLTLLTISFLFRKLGRQLRY LAELCCIGTLVTSATRGISTAFPTGVKLLSYLYKEALENSSNENYPVLLSLLKTSCEPYTRFIYDWVYSGVFRDVCGEFM IQVNEDYLGFRDKRYWTHGYVLISKEVEDCVPVFLKHVANEIYICGKTINLLKLCCPKHYICWSDIPVPRISVTFSLEEL KEMEKDCAVYVARMERIARHSCISKEQKALQTEIARQELIIQARETTEKVFETFKDRKLAEKLSLDTKKRELFQKLKDQY EKEQERRLTTKQEEADDDFSYAREIRDREKRLKALEEELELKTRQELIEHYSRLSEEATRKEQRALWKLQRHKLETTRLK FFLEEQKRMQDLVANFPVDICEENLGVLPDGEISHQTDNTNDAGLGNIENEKSVPEQHALHNNNDEVYTAQNCISKSESL CVDVTLPTENVHSQTSNASVLGVPSFDSNLCTPDVDIIDFLPTLPSENQEVAVVQSLVDDALISIGSDLNTDTKDKESLC ALKSDLQESSTGSEYDFKTILKPIACTQVSQGHIKIGEYSSNVQPARPRWSTHGHSSDSNIKIGNYVPDINVHQPKHSQH GHSSDSNINISDHMSDVEPRLPRLNLHGHISTGHIKVGEYASDVEPSTPRHSVHGHASQGNIKIGENVSDVKLSRPRWNI HGHVSDANIKIGENTTEIAPLRPRWNIHGHASQSHIKIGELVSDIEPSQPRRTPFGHPSQSSIPIGDQPVEKYAQKSESE VHSSNSTIQHLLYSNIPDKNKDTGGTLTDSPVPVPDQGNSNDDTEKRSSTLEQRVQAADSVCDGEASPNTAQSLPCMSDT LDLGTNGEENVGNDDHTWEKQQEYLKGLAEKYCLEKYQDSYELMSHPPVLHLYSNVMPNRFSFQTDSDIKSATDETTVQL IELLSLPVLMKYSVTAPMVSHVYLVNKAIVDYYFVELKMERHFEAMRHFLLMEDGEFAQSLSDMLFEKLGSGQTPSELLN PLVLNSILNKALQYSLHGDSSLASNLTFALKYLPEVFTPTAPDALSCLELKYKVDWPLNIVITDTCMNKYSRIFSFLLQL KHMVWTLRDVWFHLKRTALVNQASNSVQYRQLQLYRHEMQHFVKVIQGYIANQILHVTWCEFRNKLSAVSNLEEIYKTHA DYLNKALFRGLLTEKAAPLMNIIHSIFSLILKFRLQLISQSWICDTGKQMAVHPNFGLMQQSYNTFKYYSDFLFEVVSKL VNRGYQPHLEDFLLRINFNSYYKQS Q9DDA7 Tubulin gamma-1 chain Xenopus laevis 0.051226719 14 LEVO MPREIITLQLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDLEPRVIHSILNS PYANLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCHSIAGGTGSGLGSYLLERLNDR YPKKLVQTYSVFPNQDEMSHVVVQPYNSLLTLKRLTQNADCVVVLDNTALNRIATDRLHIQNPSFSQINQLVSTIMSAST TTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAI LNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQVALSRKSPYLPSAHRVSGLMMANHTNISSLFERTCRQYDKLRK REAFLEQFRKEDIFKDNFDELDNSREIVQQLIDEYHAATRPDYISWGTQDK P23330 Gamma-tubulin complex component Xenopus laevis 0.117577633 1 LEVO MAHWTRFERDQEGDIKKLVSLMSGIQDDQDGNFQQALQFAWSNFRFHRYLDVSSHTVLRTLEGIFEKLVVHSDLEKAESW KRLTEEFLLLPLPNTEGTKTDSHFAVLSLLLCLSDSPSNHDYTEKPRKKENDEQEPFDWGKYLREGEDIEFSPDADTPEW SEASEEEDAQEPPSREDSGIQVDRTPLEDPEKKGAPPLVSWKVGEPDARSWLEQHIVHQYWTSRAPRFSHSSHLHSNLSA IWDQHLYTTDPLYTPDDKTIVTETQVIRETLWLLSGVKKLLIFQLNDGKVNVRNDIIVTHMTQNCLRSVLEQIAAYGQVV FRLQKFIDEITGHGSEVPLPGTLPTAKKTTEAPFRTYQAFMWALYKYFISFKEELTEIEKCIINKDETVTLAIVLDKLAP RLAQLKVLHRVFSTGIAEVPPDTRNVVRASHLLNTLYKAILDYDNVGEASEQTVSLLFCLWVETVRPYLEIVDEWIVHGN LFDPAKEFIIQRNKDVPFNHRDFWYATYTLYSVSEKTENEDKMSDNASASSGSDQAPAGRQHTMVSFLKPVLKQIIMAGK SMQLLKNLKCRTALQQDSSRDSDRKSLYTLFLESVQSRLQHGNDSVPDIITEQQVNKLSLIKMQSIVAKHLELDEVHDPL LAINFVRLYLEQSDFLETFTCNEVCVDRSSESVTCQSFELTLRSCLYPHIGKQYLECCGNLMYTLKKDYRLVEYLQAMRN FFLLEAGDTMYDFYTPIFDKIREKEPWLNLSYLNVQIQEAVGQRYPDDSTRLSVSFESVDLAKKKLPVHTLDGLILSYKV PWPVDIVISSECQKIYNQVFLLLLLIKWAKYSLDVLQFNELGNASENESTKEGATVEPFPLPPLTSPSEPKGQQIHRMFL LRVKLMHFVNSLHNYLMTRILHSTGLEFQHQVEEAKDLDQLIKIHYRYLSTIHDRCLLREKVSSVKEAIMKVLNVVLMFA DRWHAGLGAWKKESIVKMESDFTNCHKFLVKVLNKAVCRGSFPHLESLALSLMAGMEQS A0A1L8HGZ5 Gamma-tubulin complex component Xenopus laevis 0.07612296099999999 2 LEVO MIHELLLALSGYPGSIFTWNKRTGLQVSQDIPFLHPGETSVLNRLCKLGTDYIRFTEFIEQYTGHVQQQDHHPSQQGQVG LHGIYLRAFCRGLDSILQPYRQALLDLEQEFLADPHLSISHINYSLDQFHLLFPSIMVVVEQIKSQKIHGCQILETVYKH SCGGLPPVRSALEKTLAVCHGVMYKQLSAWMLHGLLLDQYEEFFVRQGSSSGNLAAAFEEEEDDLGIGGLTGKQLRELQD LRLIEEENMLAPSLKQFSLRAEMLPSYIPVRVAEKILFVGESVQMFENQNVNMSRTGSILKNQEDTFAAELHRLKQQPLF SLVDFESVLDRIRSTVAEHLWKLMVEESDLLGQLKIIKDFYLLGRGELFQAFIDVAQNMLKTPPTAVTEHDVNVAFQLSA HKVLLDDDNLLPLLNLTIDYHGKEHKDTSQPREGPFRDMSPREAPTSGWAALGLSYKVQWPLHILFTPAVLEKYNVVFKY LLSVRRVQSELQHCWALQMQRKHLESNKTDAIKWRLQNHMAFLVDNLQYYLQVDVLESQFSQLLQQINSTRDFESIRLAH DHFLSNLLAQSFILLKPVFHCLNEILELCHSFCSLVSQNLGPLDERGAGQLDILVKGFSCQSSLLFRILSSVRNHQINPD LAQLLLRLDYNKYYTQAGGTLGSFGL Q642S3 Belt helix 17 Xenopus laevis 0.0013684939999999998 1 LEVO AAAAAAAAAAAAAAAAAAA Actin, cytoplasmic 1 Xenopus laevis 0.041812683999999996 1 LEVO MEDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWD DMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVT HTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITAL APSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF O93400 singleParticle particle 0.011 8.0 1.0 MgCl2 magnesium chloride 1.0 GTP Guanosine triphosphate 100.0 NaCl Sodium Chloride 1.0 EGTA Ethylene glycol tetraacetic acid 50.0 HEPES piperazineethanesulfonic acid 0.02 C58H114O26 Tween 20 0.1 gamma-tubulin antigenic C-terminal peptide2 COPPER 300 CARBON HOLEY GLOW DISCHARGE 20 ETHANE 70 295 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.5 3.5 42000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 4 9463 46.0 1 5482328

3D initial model from manually selected particles in Relion

C1 4.8 FSC 0.143 CUT-OFF RELION 3.0 Beta 46096 MAXIMUM LIKELIHOOD RELION 3.0 Beta MAXIMUM LIKELIHOOD RELION 3.0 Beta RELION 3.0 Beta emd_10491.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 537.6 537.6 537.6 90.0 90.0 90.0 X Y Z -0.07939351 0.247138 0.0008742602 0.006880397 2.1 2.1 2.1 0.04 AUTHOR ::::EMDATABANK.org::::EMD-10491:::: Cryo-EM single particle analysis reconstruction of the vertebrate gamma-Tubulin Ring Complex 3RIP PDB experimental model FLEXIBLE FIT REAL emd_10491_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 537.6 537.6 537.6 90.0 90.0 90.0 X Y Z -0.44612977 0.8545948 0.010161957 0.01787147 2.1 2.1 2.1 AUTHOR ::::EMDATABANK.org::::EMD-10491:::: Cryo-EM single particle analysis reconstruction of the vertebrate gamma-Tubulin Ring Complex filtered according to local resolution