Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U12 snRNP part

2024-10-23 REL PDBc PDBj PDBc 2024-02-04 2024-03-13 2024-03-13 2024-10-23 National Natural Science Foundation of China (NSFC) 32171214 China National Natural Science Foundation of China (NSFC) 31930059 China National Natural Science Foundation of China (NSFC) 32100987 China Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U12 snRNP part Bai R Yuan M Zhang P Luo T Shi Y Wan R spliceosome, minor spliceosome, U11 snRNP, U12 snRNP, U4atac, U6atac, CENATAC, TXNL4B, U11 snRNA, minor tri-snRNP, U12-type intron, SPLICING/RNA, SPLICING-RNA complex Bai R Yuan M Zhang P Luo T Shi Y Wan R Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science US 383 1245 1252 2024 38484052 doi:10.1126/science.adn7272 1095-9203 0038 SCIEAS 8y7e FULLOVERLAP human minor pre-B complex (U12 snRNP part) human minor pre-B complex (U12 snRNP part) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Homo sapiens 1.8 pre-mRNA Homo sapiens 0.08952265599999999 1 GAAUACACGGAAUUCGAGCUCGCCCACUCUUGGAUCGGAAACCCGUCGGCCUCCGAAAUAUCCUUUUCUAGCAUGUAGAA CUGGUUACCUGCAGCCCAAGCUUGCUGCGAUAUCCGUACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGG GUACGACUAGUAGAUCUCGUACACCAUCAGGGUACGGAAUUCUCUAGACACGUCUAGGGCGCAGUAGUCCAGGGUUUCCU UGAUGAUGUCAUAUCCUUAACUCAUUGUCCCUUUUUUUUC Splicing factor 3B subunit 1 Homo sapiens 0.14610490599999998 1 LEVO MAKIAKTHEDIEAQIREIQGKKAALDEAQGVGLDSTGYYDQEIYGGSDSRFAGYVTSIAATELEDDDDDYSSSTSLLGQK KPGYHAPVALLNDIPQSTEQYDPFAEHRPPKIADREDEYKKHRRTMII(SEP)PERLDPFADGGKTPDPKMNARTYMDVM REQHLTKEEREIRQQLAEKAKAGELKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAETPGHTPSLRWDETP GRAKGSETPGATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRWDETPKTERDTPGHGSGWAETPRT DRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPIGTPAMNMATPTPGHIMSMTPEQLQAWRWEREIDERN RPLSDEELDAMFPEGYKVLPPPAGYVPIRTPARKLTATPTPLGGMTGFHMQTEDRTMKSVNDQPSGNLPFLKPDDIQYFD KLLVDVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLMSPTLEDQERHLLVKVI DRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAAGLATMISTMRPDIDNMDEYVRNTTARAFAVVA SALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHLRSLVEIIEHGLVDEQQKVRTISALAIAALAEAA TPYGIESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSPDEEMKKIVLKVVKQCC GTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVELANKVGAAEIISRIVDDLKDEAEQYRKMVMETIEKIM GNLGAADIDHKLEEQLIDGILYAFQEQTTEDSVMLNGFGTVVNALGKRVKPYLPQICGTVLWRLNNKSAKVRQQAADLIS RTAVVMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVIGMHKMTPPIKDLLPRLTPILKNRHEKVQENCI DLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYIAKAIGPHDVLATLLNNLKVQERQNRVCTTVAI AIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTASAVVQHMS LGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPCRMLQYCLQGLFHPARKVRDVYWKIYNSIYIGS QDALIAHYPRIYNDDKNTYIRYELDYIL O75533 Splicing factor 3B subunit 2 Homo sapiens 0.100377812 1 LEVO MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQTGIVLNRPVLRGEDGDKAAP PPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFPMAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQ EERAKQQGDHSLKEHELLEQQKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDARSSLGQSASETEEDTVSVSK KEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGSDSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVK KEKEKEPEKLDKLENSAAPKKKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREALQEKEEQKTMKSKMREKVRPK MGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETRLKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYG PPPSYPNLKIPGLNSPIPESCSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSETPQLFTVLPEKRTATVGGAMM GSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAMTQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQP QDSRGGSKKYKEFKF Q13435 Splicing factor 3B subunit 3 Homo sapiens 0.135798828 1 LEVO MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFGVIRSLMAFRLTGGTKDYIVV GSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQFLAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEA HKANTLVYHVVGVDVGFENPMFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFFFLAQTEQGDIFKITLETDED MVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQIAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDE LDSLSPILFCQIADLANEDTPQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPGKKTIVKCAVNQRQVVIALTG GELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQRSRFLAVGLVDN(TPO)VRIISLDPSDCLQPLSMQALPAQ PESLCIVEMGGTEKQDELGERGSIGFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMS SRSWLSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFPLQYTPRKFVIHPESNN LIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAAAFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNT LDLVQLEQNEAAFSVAVCRFSNTGEDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQ GRVLIGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQLIIFADDTYPRWVTTA SLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRGLLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSES LVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEE LDRTPPEVSKKLEDIRTRYAF Q15393 Splicing factor 3B subunit 4 Homo sapiens 0.044436569999999995 1 LEVO MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMNMIKLY GKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE AMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLG HPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGP LPPPRPTPRPPVPPRGPLRGPLPQ Q15427 Splicing factor 3B subunit 6 Homo sapiens 0.014606899999999999 1 LEVO MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF NVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK Q9Y3B4 PHD finger-like domain-containing protein 5A Homo sapiens 0.012427523999999999 1 LEVO MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEK DRDGCPKIVNLGSSKTDLFYERKKYGFKKR Q7RTV0 Splicing factor 3B subunit 5 Homo sapiens 0.010149369 1 LEVO MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENESKARVRFNLMEKMLQPCGPPA DKPEEN Q9BWJ5 U12 snRNA Homo sapiens 0.048353625 1 AUGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUUCGGGGUGACGCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUU GAGCGGGUAAAGGUCGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCCUGGGAGUUGCGAUCUGCCCG L43846.1 Small nuclear ribonucleoprotein Sm D3 Homo sapiens 0.013940308 1 LEVO MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNA PMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR P62318 Small nuclear ribonucleoprotein-associated proteins B and B' Homo sapiens 0.024642131 1 LEVO MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSM TVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATAS IAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP P14678 Small nuclear ribonucleoprotein Sm D1 Homo sapiens 0.013310653 1 LEVO MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLL VDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR P62314 Small nuclear ribonucleoprotein Sm D2 Homo sapiens 0.013551928 1 LEVO MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKS GKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK P62316 Small nuclear ribonucleoprotein E Homo sapiens 0.010817601 1 LEVO MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLK GDNITLLQSVSN P62304 Small nuclear ribonucleoprotein F Homo sapiens 0.009734171 1 LEVO MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEE DGEMRE P62306 Small nuclear ribonucleoprotein G Homo sapiens 0.008508084 1 LEVO MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALERV P62308 Sodium channel modifier 1 Homo sapiens 0.025993537 1 LEVO MSFKREGDDWSQLNVLKKRRVGDLLASYIPEDEALMLRDGRFACAICPHRPVLDTLAMLTAHRAGKKHLSSLQLFYGKKQ PGKERKQNPKHQNELRREETKAEAPLLTQTRLITQSALHRAPHYNSCCRRKYRPEAPGPSVSLSPMPPSEVKLQSGKISR EPEPAAGPQAEESATVSAPAPMSPTRRRALDHYLTLRSSGWIPDGRGRWVKDENVEFDSDEEEPPDLPLD Q9BWG6 ZINC ION 6.5409e-05 4 ZN singleParticle particle 0.2 7.9 Quantifoil R1.2/1.3 GOLD 300 CARBON CONTINUOUS PLASMA CLEANING NITROGEN FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 3.0 81000.0 NITROGEN GATAN K3 (6k x 4k) 50.0 1 4.66 FSC 0.143 CUT-OFF 107724 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_39013.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 549.9904 549.9904 549.9904 90.0 90.0 90.0 X Y Z -0.007419861 0.029011318 0.0002686663 0.0012926064 1.0742 1.0742 1.0742 0.004 AUTHOR ::::EMDATABANK.org::::EMD-39013:::: Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region. emd_39013_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 549.9904 549.9904 549.9904 90.0 90.0 90.0 X Y Z -0.014404845 0.037319392 0.0006591633 0.0019450221 1.0742 1.0742 1.0742 AUTHOR ::::EMDATABANK.org::::EMD-39013:::: Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region. emd_39013_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 549.9904 549.9904 549.9904 90.0 90.0 90.0 X Y Z -0.0173515 0.03819196 0.0007783522 0.0021302558 1.0742 1.0742 1.0742 AUTHOR ::::EMDATABANK.org::::EMD-39013:::: Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region.