7ABG: Human pre-Bact-1 spliceosome

Human pre-Bact-1 spliceosome. Determined by electron microscopy at 7.8 Å resolution. Released 23 Dec 2020.

Method
Electron microscopy
Resolution
7.8 Å
Organisms
Homo sapiens, synthetic construct
Chains
58
Atoms
73,818
Mol. weight
2762.07 kDa
Ligands
IHP, GTP, MG, GTG
Released
23 Dec 2020

Explore 7ABG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ABG contains 534 α-helices and 507 β-strands across 54 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 1 helix, 9 β-strands

ElementResiduesLengthSheet
α-helix230-2367
β-strand238179
β-strand243179
β-strand252180
β-strand261181
β-strand263-264282
β-strand273181
β-strand307-314880
β-strand320-327880
β-strand368-369282
Chain 4: 24 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix3-75
α-helix8-2720
α-helix33-5826
α-helix62-7211
α-helix79-879
α-helix103-1086
β-strand112111
β-strand115111
α-helix119-1213
α-helix126-1283
α-helix132-1343
α-helix143-15311
α-helix160-1678
α-helix182-19918
α-helix206-21914
α-helix221-2233
β-strand284112
β-strand289112
α-helix294-3007
α-helix304-3074
α-helix318-33316
α-helix335-35016
α-helix353-3619
α-helix394-4007
β-strand406-408313
β-strand414-416313
α-helix419-4268
α-helix429-43810
α-helix452-46211
α-helix489-49810
Chain 9: 2 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix22-243
β-strand28-3367
β-strand37-46107
β-strand52-63127
β-strand76-87127
α-helix89-913
β-strand92-9657
Chain a: 1 helix, 5 β-strands
ElementResiduesLengthSheet
α-helix27-3711
β-strand42-4656
β-strand51-5996
β-strand65-7396
β-strand93-10196
β-strand106-11056
Chain A: 91 helices, 57 β-strands
ElementResiduesLengthSheet
α-helix65-695
α-helix85-9410
α-helix98-1025
α-helix109-1113
β-strand117-1204114
β-strand127-1282114
α-helix131-1333
α-helix137-15721
α-helix234-24310
α-helix260-26910
α-helix310-3156
α-helix317-3204
α-helix370-3712
α-helix374-3785
α-helix399-4035
α-helix404-4063
α-helix428-4314
α-helix441-45919
α-helix476-4783
β-strand483-4864114
α-helix489-51022
β-strand516-5172115
β-strand525-5262115
α-helix535-5373
α-helix544-56522
α-helix573-58614
α-helix591-5944
α-helix598-61619
α-helix633-65725
α-helix678-69518
α-helix708-72114
α-helix733-75927
α-helix771-79626
α-helix803-82018
β-strand8251116
α-helix835-85016
α-helix860-87213
α-helix874-88714
α-helix893-8942
β-strand895-8995117
β-strand906-9105117
α-helix913-93321
β-strand9401118
α-helix947-96014
β-strand973-9808118
α-helix990-100011
β-strand10011116
α-helix1003-101210
β-strand10181117
α-helix1038-105316
α-helix1056-10627
α-helix1077-10826
β-strand1085-10906118
β-strand1094-11018118
α-helix1103-111614
α-helix1144-115613
β-strand1174-11785118
β-strand1185-11884119
β-strand1193-11986119
β-strand1216-12172119
β-strand1224-12318119
α-helix1234-124815
α-helix1256-127015
α-helix1282-129514
α-helix1314-13174
α-helix1334-13363
α-helix1337-13393
β-strand1341-13455120
β-strand1350-13545120
α-helix1368-13714
α-helix1375-139824
α-helix1405-14084
α-helix1409-14113
α-helix1427-14304
α-helix1436-14416
α-helix1442-14454
α-helix1468-147710
α-helix1480-14856
α-helix1529-15379
α-helix1539-15424
β-strand1553-15542121
β-strand1561-15622121
α-helix1567-157610
α-helix1581-159919
α-helix1602-16043
β-strand1606-16083122
β-strand16111122
β-strand1629-163810122
β-strand1642-16443122
β-strand1656-16627122
β-strand1665-16662123
α-helix1671-16733
α-helix1676-168914
β-strand1700-17012122
β-strand1704-17063123
β-strand1711-17133123
β-strand1715-17173122
α-helix1718-17192
α-helix1723-173412
α-helix1738-175114
β-strand1779-17813124
β-strand1788-17914125
β-strand1799-18024125
β-strand1805-18106124
β-strand1816-18227124
α-helix1824-18263
α-helix1833-185018
α-helix1854-18563
β-strand1861-18633124
α-helix1870-18756
β-strand1884-18852124
α-helix1893-18975
α-helix1900-19078
β-strand1914-19185124
α-helix1921-19255
α-helix1929-194517
α-helix1947-19537
α-helix1969-19702
α-helix1973-199523
α-helix2004-20107
α-helix2072-208110
α-helix2086-20883
β-strand2090-20912126
β-strand2103-21075126
α-helix2108-211710
α-helix2123-21242
β-strand2125-21317126
α-helix2132-21332
β-strand2139-21468126
β-strand21501127
β-strand2151-21522128
β-strand2157-21582128
α-helix2162-21643
β-strand2173-21819126
α-helix2190-220213
β-strand2212-22176126
β-strand2223-22286126
α-helix2232-22409
α-helix2253-22553
β-strand22581126
β-strand2260-22645126
β-strand2270-22712126
β-strand2273-22742129
β-strand22801127
β-strand2296-22972129
α-helix2300-23034
α-helix2311-23144
α-helix2321-23233
Chain A1: 7 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix8-103
α-helix13-153
α-helix29-368
β-strand41-45576
α-helix53-608
α-helix61-633
β-strand66-73876
β-strand80-88976
α-helix91-10010
β-strand105-106277
β-strand109-110277
β-strand112-115476
β-strand125176
α-helix135-1384
β-strand143178
β-strand148178
Chain A2: 1 helix, 5 β-strands
ElementResiduesLengthSheet
α-helix14-185
β-strand22-2767
β-strand32-4097
β-strand46-56117
β-strand64-76137
β-strand81-8667
Chain A3: 3 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix6-83
β-strand12-1767
β-strand22-3097
α-helix351
β-strand36-4387
β-strand54-6297
α-helix64-663
β-strand67-7267

46 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Nuclear cap-binding protein subunit 1A5protein790Homo sapiensQ09161 (AlphaFold model)
U6 snRNA-associated Sm-like protein LSm7A2protein103Homo sapiensQ9UK45 (AlphaFold model)
Splicing factor 3B subunit 6zprotein125Homo sapiensQ9Y3B4 (AlphaFold model)
Splicing factor 3A subunit 2Fprotein464Homo sapiensQ15428 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa proteinDprotein357Homo sapiensQ96DI7
U2 small nuclear ribonucleoprotein A'Wprotein255Homo sapiensP09661
U2 small nuclear ribonucleoprotein B''Bprotein225Homo sapiensP08579
U5 small nuclear ribonucleoprotein 200 kDa helicasesprotein2136Homo sapiensO75643
Protein BUD31 homologQprotein144Homo sapiensP41223
Nuclear cap-binding protein subunit 2A1protein156Homo sapiensP52298
U5 snRNA5RNA116Homo sapiens
Cell division cycle 5-like proteinLprotein802Homo sapiensQ99459

39 more molecules are not listed.

Sequence of entity 1 (A5), FASTA
>7ABG_1 Nuclear cap-binding protein subunit 1 (chains A5)
MSRRRHSDENDGGQPHKRRKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEAD
LPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANN
YNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWV
GKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLK
KDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG
PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELF
QLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHH
LSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPAN
PTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQM
IAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELE
EAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMI
LTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILA
VFQQFCALQA
Sequence of entity 2 (A2), FASTA
>7ABG_2 U6 snRNA-associated Sm-like protein LSm7 (chains A2)
MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDD
QYKLTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDA
Sequence of entity 3 (z), FASTA
>7ABG_3 Splicing factor 3B subunit 6 (chains z)
MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA
YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN
TDPPK
Sequence of entity 4 (F), FASTA
>7ABG_4 Splicing factor 3A subunit 2 (chains F)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN
Sequence of entity 5 (D), FASTA
>7ABG_5 U5 small nuclear ribonucleoprotein 40 kDa protein (chains D)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ
Sequence of entity 6 (W), FASTA
>7ABG_6 U2 small nuclear ribonucleoprotein A' (chains W)
MVKLTAELIEQAAQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGF
PLLRRLKTLLVNNNRICRIGEGLDQALPCLTELILTNNSLVELGDLDPLASLKSLTYLSI
LRNPVTNKKHYRLYVIYKVPQVRVLDFQKVKLKERQEAEKMFKGKRGAQLAKDIARRSKT
FNPGAGLPTDKKKGGPSPGDVEAIKNAIANASTLAEVERLKGLLQSGQIPGRERRSGPTD
DGEEEMEEDTVTNGS
Sequence of entity 7 (B), FASTA
>7ABG_7 U2 small nuclear ribonucleoprotein B'' (chains B)
MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
NKKPGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
Sequence of entity 8 (s), FASTA
>7ABG_8 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains s)
MADVTARSLQYEYKANSNLVLQADRSLIDRTRRDEPTGEVLSLVGKLEGTRMGDKAQRTK
PQMQEERRAKRRKRDEDRHDINKMKGYTLLSEGIDEMVGIIYKPKTKETRETYEVLLSFI
QAALGDQPRDILCGAADEVLAVLKNEKLRDKERRKEIDLLLGQTDDTRYHVLVNLGKKIT
DYGGDKEIQNMDDNIDETYGVNVQFESDEEEGDEDVYGEVREEASDDDMEGDEAVVRCTL
SANLVASGELMSSKKKDLHPRDIDAFWLQRQLSRFYDDAIVSQKKADEVLEILKTASDDR
ECENQLVLLLGFNTFDFIKVLRQHRMMILYCTLLASAQSEAEKERIMGKMEADPELSKFL
YQLHETEKEDLIREERSRRERVRQSRMDTDLETMDLDQGGEALAPRQVLDLEDLVFTQGS
HFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKT
LNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIY
IAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKG
GERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYED
VATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQ
VLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPY
GFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGR
WTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDM
LNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTA
ALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSL
SSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMAD
MVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVV
KKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKV
ELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFE
PLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESL
YQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYIT
PMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWK
QRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDV
AHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVI
VFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYL
HEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYP
IYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEI
VTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSK
CISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPI
RHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAI
RLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVE
SVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQ
LEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATG
AHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD
Sequence of entity 9 (Q), FASTA
>7ABG_9 Protein BUD31 homolog (chains Q)
MPKVKRSRKAPPDGWELIEPTLDELDQKMREAETEPHEGKRKVESLWPIFRIHHQKTRYI
FDLFYKRKAISRELYEYCIKEGYADKNLIAKWKKQGYENLCCLRCIQTRDTNFGTNCICR
VPKSKLEVGRIIECTHCGCRGCSG
Sequence of entity 10 (A1), FASTA
>7ABG_10 Nuclear cap-binding protein subunit 2 (chains A1)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ
Sequence of entity 11 (5), FASTA
>7ABG_11 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGCCUUGCCUUGGCAAGGCUA
Sequence of entity 12 (L), FASTA
>7ABG_12 Cell division cycle 5-like protein (chains L)
MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKK
TEWSREEEEKLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKAAQRDNEEETTDDP
RKLKPGEIDPNPETKPARPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEAR
RLAALQKRRELRAAGIEIQKKRKRKRGVDYNAEIPFEKKPALGFYDTSEENYQALDADFR
KLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAILQTSGVSEFTKKRSKLVLPAP
QISDAELQEVVKVGQASEIARQTAEESGITNSASSTLLSEYNVTNNSVALRTPRTPASQD
RILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
EGLTPRSGTTPKPVINSTPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGL
LGLPAPKNDFEIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKA
VQKDLPRPSEVNETILRPLNVEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNKKG
KTVGFGTNNSEHITYLEHNPYEKFSKEELKKAQDVLVQEMEVVKQGMSHGELSSEAYNQV
WEECYSQVLYLPGQSRYTRANLASKKDRIESLEKRLEINRGHMTTEAKRAAKMEKKMKIL
LGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLECLKEDVQRQQER
EKELQHRYADLLLEKETLKSKF

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P61
GTPGuanosine-5'-triphosphateC10 H16 N5 O14 P31
MGMagnesium ionMg1
GTG7-methyl-guanosine-5'-triphosphate-5'-guanosineC21 H30 N10 O18 P31

Primary citation

Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Townsend, C., Leelaram, M.N., Agafonov, D.E. et al. Science (2020) 370. DOI 10.1126/science.abc3753 · PubMed

Other PDB entries of the same protein (UniProt Q09161 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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