Human nuclear exosome-MTR4 RNA complex

2024-03-13 REL RCSB RCSB RCSB 2018-04-22 2018-05-16 2018-06-20 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM118080 United States Howard Hughes Medical Institute (HHMI) United States Human nuclear exosome-MTR4 RNA complex - overall reconstruction Weick E-M Lima CD RNA exosome, RNA degradation, ribonuclease, helicase, SF2, RNA-protein complex, translocase, nuclear, HYDROLASE Weick EM Puno MR Januszyk K Zinder JC DiMattia MA Lima CD Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. Cell 173 1663 2018 29906447 doi:10.1016/j.cell.2018.05.041 1097-4172 EMD-7809 other EM volume EMD-7810 other EM volume EMD-7812 other EM volume EMD-7813 other EM volume EMD-7814 other EM volume EMD-7815 other EM volume EMD-7818 other EM volume EMD-7819 other EM volume 6d6q FULLOVERLAP Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Human C1D/Rrp47 also in the sample, but was not observed in density

Homo sapiens 0.69 Exosome complex component RRP45 Homo sapiens 0.052828019999999996 1 Escherichia coli LEVO MGSSHHHHHHSQDPNSHMKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCEL VSPKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDG NIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVI AMNKHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEKAPI DTSDVEEKAEEIIAEAEPPSEVVSTPVLWTPGTAQIGEGVENSWGDLEDSEKEDDEGGGDQAIILDGIKMDTGVEVSDIG SQELGFHHVGQTGLEFLTSDAPIILSDSEEEEMIILEPDKNPKKIRTQTTSAKQEKAPSKKPVKRRKKKRAAN Q06265 Exosome complex component RRP41 Homo sapiens 0.026831473 1 Escherichia coli LEVO MADPMAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQY SSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDF VCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHV REASILLGD Q9NPD3 Exosome complex component RRP43 Homo sapiens 0.030285761999999997 1 Escherichia coli LEVO DPMAAGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGY VVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLA ALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKP GGSGLTGAKLQDCMSRAVTRHKEVKKLMDEVIKSMKPK Q96B26 Exosome complex component RRP46 Homo sapiens 0.025480212999999998 1 Escherichia coli LEVO SLMEEETHTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEV ILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACA LDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSKS Q9NQT4 Exosome complex component RRP42 Homo sapiens 0.032072633 1 Escherichia coli LEVO DPMASVTLSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGY LEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKA ALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTC MRKVGKGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEESLGPKRQKVGFLG Q15024 Exosome complex component MTR3 Homo sapiens 0.028267127 1 Escherichia coli LEVO MPGDHRRIRGPEESQPPQLYAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGG PAGAGGEAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAA ALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEA VRLGLEGCQRLYPVLQQSLVRAARRRGAAAQP Q5RKV6 Exosome complex component RRP40 Homo sapiens 0.029796371 1 Escherichia coli LEVO DPMAEPASVAAESLAGSRARAARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRL LVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQ VGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLHPLEIVFGMNGRIW VKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES Q9NQT5 Exosome complex component RRP4 Homo sapiens 0.033184371 1 Escherichia coli LEVO DPHMAMEMRLPVARKPLSERLGRDTKKHLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYI GEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLH TRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRL RNCIISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRLLEQEG Q13868 Exosome complex component CSL4 Homo sapiens 0.021690971 1 Escherichia coli LEVO DPMAPPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSI NSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHS ESGIQMVPISWCEMQCPKTHTKEFRKVARVQPEFLQT Q9Y3B2 Exosome component 10 Homo sapiens 0.08675485899999999 1 Escherichia coli LEVO SMAPPSTREPRVLSATSATKSDGEMVLPGFPDADSFVKFALGSVVAVTKASGGLPQFGDEYDFYRSFPGFQAFCETQGDR LLQCMSRVMQYHGCRSNIKDRSKVTELEDKFDLLVDANDVILERVGILLDEASGVNKNQQPVLPAGLQVPKTVVSSWNRK AAEYGKKAKSETFRLLHAKNIIRPQLKFREKIDNSNTPFLPKIFIKPNAQKPLPQALSKERRERPQDRPEDLDVPPALAD FIHQQRTQQVEQDMFAHPYQYELNHFTPADAVLQKPQPQLYRPIEETPCHFISSLDELVELNEKLLNCQEFAVNLEHHSY RSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLG RHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWERGNGQPVQLQVVWQRSRDICLK KFIKPIFTDESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVP PLVRQQINEMHLLIQQAREMPLLKSEVAAGVKKSGPLPSAERLENVLFGPHDCSHAPPDGYPIIPTSGSVPVQKQASLFP DEKEDNLLGSRGSGSGSGSGSVSQAAKFDPSTKIYEISNRWKLAQVQVQKDSKEAVKKKAAEQTAAREQAKEACKAAAEQ AISVRQQVVLENAAKKRERATSDPRTTEQKQEKKRLKISKK Q01780 Q01780 3.1.13.- Exosome complex exonuclease RRP44 Homo sapiens 0.10926792999999999 1 Escherichia coli LEVO GSMLKSKTFLKKTRAGGVMKIVREHYLRDDIGCGAPGCAACGGAHEGPALEPQPQDPASSVCPQPHYLLPDTNVLLHQID VLEDPAIRNVIVLQTVLQEVRNRSAPVYKRIRDVTNNQEKHFYTFTNEHHRETYVEQEQGENANDRNNRAIRVAAKWYNE HLKKMSADNQLQVIFITNDRRNKEKAIEEGIPAFTCEEYVKSLTANPELIDRLACLSEEGNEIESGKIIFSEHLPLSKLQ QGIKSGTYLQGTFRASRENYLEATVWIHGDSEENKEIILQGLKHLNRAVHEDIVAVELLPKSQWVAPSSVVLHDEGQNEE DVEKEEETERMLKTAVSEKMLKPTGRVVGIIKRNWRPYCGMLSKSDIKESRRHLFTPADKRIPRIRIETRQASTLEGRRI IVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSV DPPGCTDINDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRL AFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVR FHMDSETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTA KSLAESLDQAESPTFPYLNTLLRILATRCMMQAVYFCSGMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGAD CTYPELTDKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSNGIVSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEK DKPNPQLIYDDEIPSLKIEDTVFHVFDKVKVKIMLDSSNLQHQKIRMSLVEPQIPGISIPTDTSNMDLNGPKKKKMKLGK Q9Y2L1 3.1.13.- M-phase phosphoprotein 6 Homo sapiens 0.019267961 1 Escherichia coli LEVO DPMAAERKTRLSKNLLRMKFMQRGLDSETKKQLEEEEKKIISEEHWYLDLPELKEKESFIIEEQSFLLCEDLLYGRMSFR GFNPEVEKLMLQMNAKHKAEEVEDETVELDVSDEEMARRYETLVGTIGKKFARKRDHANYEEDENGDITPIKAKKMFLKP QD Q99547 Exosome RNA helicase MTR4 Homo sapiens 0.11822496099999999 1 Escherichia coli LEVO SGDMADAFGDELFSVFEGDSTTAAGTKKDKEKDKGKWKGPPGSADKAGKRFDGKLQSESTNNGKNKRDVDFEGTDEPIFG KKPRIEESITEDLSLADLMPRVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQREAIQCVDNNQSV LVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLY RGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTDYRPTPLQ HYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDAGDLAKGDQKGRKGGTKGPSNVFKIVKMIMERNFQPVIIFSFSKK DCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETIEILFSEGLIK ALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSAD PLNSAFHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEESVVIYYKIRQQLAKLG KEIEEYIHKPKYCLPFLQPGRLVKVKNEGDDFGWGVVVNFSKKSNVKPNSGELDPLYVVEVLLRCSKESLKNSATEAAKP AKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQKV EAFEHRMYSHPLHNDPNLETVYTLCEKKAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVA CEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEET YLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVFA ASLYL P42285 3.6.4.13 RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3') synthetic construct 0.005143175 1 AGCACCGUAAAGACGC DNA/RNA (62-MER) synthetic construct 0.019487074 1 (DG)(DC)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DC)(DG)(DG)(DT)(DG)(DC)(DT)CACCACACCACACCAC ACCACACCACACCACACCACACAAAAAAAA polydeoxyribonucleotide/polyribonucleotide hybrid MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 1 ZN PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER 0.000506196 1 ANP singleParticle particle 1.0 8.0 20.0 Tris-HCl 100.0 NaCl sodium chloride 0.5 MgCl2 magnesium chloride 2.0 AMPPNP 1.0 BME 0.05 Chapso Quantifoil R2/2 GOLD GLOW DISCHARGE 60 AIR 0.037 ETHANE 298 FEI VITROBOT MARK IV

30 sec wait time, 2.5 sec blot time.

Sample was monodisperse upon elution from gel filtration prior to vitrification.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1439 85.23 1 278185

Ab initio model determination

1 3.45 FSC 0.143 CUT-OFF RELION 2.1b1

Focused refinements with five strategies required to achieve final model

122703 RANDOM ASSIGNMENT cryoSPARC 0.6.1 from 0.6.1 to 0.6.5 PROJECTION MATCHING RELION 2.1b1 4 271036.0 RELION 2.1b1 emd_7808.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 410.88 410.88 410.88 90.0 90.0 90.0 X Y Z -0.08375969 0.15396504 0.00014034889 0.0025395288 1.07 1.07 1.07 0.025 AUTHOR ::::EMDATABANK.org::::EMD-7808:::: Overall reconstruction for human nuclear exosome-MTR4 helicase complex BACKBONE TRACE

Models were rebuilt manually using Coot, with real space refinement with local scaling followed by Phenix real space refinement with suboptimal global scaling.

Correlation coefficient REAL 73.599999999999994