7ABH: Human pre-Bact-2 spliceosome

Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion). Determined by electron microscopy at 4.5 Å resolution. Released 9 Dec 2020.

Method
Electron microscopy
Resolution
4.5 Å
Organisms
Homo sapiens, synthetic construct
Chains
16
Atoms
17,922
Mol. weight
1029.67 kDa
Released
9 Dec 2020

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

Secondary structure: helices and β-sheets

7ABH contains 139 α-helices and 150 β-strands across 14 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: 2 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix231-2366
β-strand238142
β-strand243142
α-helix247-2493
β-strand261143
β-strand264144
β-strand273143
β-strand283145
β-strand292145
β-strand304146
β-strand307-314847
β-strand320-327847
β-strand330146
β-strand368144
Chain 1: 5 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix5-1915
α-helix24-263
β-strand37-41548
α-helix49-568
α-helix57-593
β-strand62-67648
β-strand80-84548
α-helix87-9610
β-strand108-111448
Chain 4: 5 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix394-3996
β-strand406-40838
β-strand414-41638
α-helix419-4268
α-helix429-43810
α-helix452-46110
α-helix489-4979
Chain 7: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix148-17831
Chain E: 20 helices, 99 β-strands
ElementResiduesLengthSheet
β-strand3-9712
β-strand16-20513
β-strand29-33513
β-strand37-41513
β-strand52-57613
β-strand62-68714
β-strand77-82614
β-strand86-91614
β-strand100-106714
β-strand120-123415
β-strand129-133515
β-strand136116
β-strand139-143515
β-strand144-145217
β-strand153-154217
α-helix156-1572
β-strand158-159215
β-strand165-172816
α-helix173-1742
β-strand181-188816
α-helix192-1943
β-strand207-214816
β-strand219-227916
β-strand232-238718
α-helix2391
β-strand247-252618
β-strand255-258418
α-helix264-2663
β-strand267-269318
β-strand273-274219
β-strand289-294620
β-strand299-304620
β-strand309-317920
β-strand322-3321120
β-strand336-342721
β-strand346-351621
β-strand357-361521
β-strand372-374320
β-strand386-387219
β-strand395-399521
β-strand407-413722
β-strand422-427622
α-helix430-4323
β-strand434-438522
β-strand439123
β-strand442124
β-strand445-450625
β-strand458-463626
β-strand471-477726
β-strand482-486526
β-strand493-494226
β-strand507-510427
β-strand516-520527
β-strand523-527527
β-strand533-537527
β-strand544-549628
β-strand553-558628
α-helix559-5613
β-strand562129
β-strand563-568628
β-strand574-576328
α-helix5771
α-helix5811
β-strand582129
α-helix5831
β-strand587-592630
α-helix593-5953
β-strand604-609630
β-strand613-618630
β-strand626-632730
β-strand637-644831
β-strand663-669731
β-strand674-678531
β-strand687-689331
β-strand700-706732
β-strand709-715732
β-strand721-724432
β-strand729-732432
β-strand734124
β-strand741-745525
β-strand753-758625
β-strand761-766625
β-strand775123
α-helix7841
β-strand785-790633
β-strand797-804833
α-helix809-82416
α-helix839-8446
β-strand862-869833
β-strand876-881633
β-strand886-8951034
β-strand903-911934
β-strand922-928734
β-strand942-945434
β-strand949-955735
β-strand958-963635
β-strand966-971635
β-strand978-983635
β-strand990-995636
β-strand999-1004636
β-strand1009-1015736
β-strand1020-1023436
β-strand1026137
β-strand1036-1038338
β-strand1043-1047538
β-strand1052-1057638
β-strand1088137
β-strand1090-1096738
β-strand1104112
β-strand1117-1119312
β-strand1126-1131612
α-helix1135-115117
α-helix1160-11645
β-strand1171138
β-strand1173-1174212
α-helix1176-11794
α-helix1181-11844
α-helix1187-119711
α-helix1201-121515
Chain F: 3 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix20-4122
β-strand46-4837
β-strand54-5637
β-strand61-6337
α-helix66-705
α-helix79-8911
Chain L: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix13-2513
α-helix31-355
α-helix43-5210
Chain T: 11 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix459-4613
α-helix462-4687
α-helix472-4743
α-helix477-4793
α-helix485-4928
α-helix502-5043
α-helix526-5294
α-helix533-54412
α-helix569-5768
α-helix611-6177
α-helix632-6398
β-strand651110
β-strand655110
β-strand683111
β-strand686111

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cell division cycle 5-like proteinLprotein802Homo sapiensQ99459 (AlphaFold model)
PHD finger-like domain-containing protein 5Ayprotein110Homo sapiensQ7RTV0 (AlphaFold model)
MINX M3 pre-mRNAZRNA230synthetic construct
Splicing factor 3A subunit 2Fprotein464Homo sapiensQ15428 (AlphaFold model)
Splicing factor 3A subunit 34protein501Homo sapiensQ12874 (AlphaFold model)
Splicing factor 3B subunit 1uprotein1304Homo sapiensO75533
Splicing factor 3B subunit 2Tprotein895Homo sapiensQ13435
Splicing factor 3B subunit 3Eprotein1217Homo sapiensQ15393
Splicing factor 3B subunit 4wprotein424Homo sapiensQ15427
Splicing factor 3B subunit 5xprotein86Homo sapiensQ9BWJ5
Splicing factor 3B subunit 6zprotein125Homo sapiensQ9Y3B4
Smad nuclear-interacting protein 10protein396Homo sapiensQ8TAD8

4 more molecules are not listed.

Sequence of entity 1 (L), FASTA
>7ABH_1 Cell division cycle 5-like protein (chains L)
MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKK
TEWSREEEEKLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKAAQRDNEEETTDDP
RKLKPGEIDPNPETKPARPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEAR
RLAALQKRRELRAAGIEIQKKRKRKRGVDYNAEIPFEKKPALGFYDTSEENYQALDADFR
KLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAILQTSGVSEFTKKRSKLVLPAP
QISDAELQEVVKVGQASEIARQTAEESGITNSASSTLLSEYNVTNNSVALRTPRTPASQD
RILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
EGLTPRSGTTPKPVINSTPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGL
LGLPAPKNDFEIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKA
VQKDLPRPSEVNETILRPLNVEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNKKG
KTVGFGTNNSEHITYLEHNPYEKFSKEELKKAQDVLVQEMEVVKQGMSHGELSSEAYNQV
WEECYSQVLYLPGQSRYTRANLASKKDRIESLEKRLEINRGHMTTEAKRAAKMEKKMKIL
LGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLECLKEDVQRQQER
EKELQHRYADLLLEKETLKSKF
Sequence of entity 2 (y), FASTA
>7ABH_2 PHD finger-like domain-containing protein 5A (chains y)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR
Sequence of entity 3 (Z), FASTA
>7ABH_3 MINX M3 pre-mRNA (chains Z)
GGGAGACGGAAUUCGAGCUCGCCCACUCUUGGAUCGGAAACCCGUCGGCCUCCGAACGGU
AAGAGCCUAGCAUGUAGAACUGGUUACCUGCAGCCCAAGCUUGCUGCACGUCUAGGGCGC
AGUAGUCCAGGGUUUCCUUGAUGAUGUCAUACUUAUCCUGUCCCUUUUUUUUCCACAGCU
CGCGGUUGAGGACAAACUCUUCGCGGUCUUUCCAGUGGGGAUCCAAUAUC
Sequence of entity 4 (F), FASTA
>7ABH_4 Splicing factor 3A subunit 2 (chains F)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN
Sequence of entity 5 (4), FASTA
>7ABH_5 Splicing factor 3A subunit 3 (chains 4)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL
Sequence of entity 6 (u), FASTA
>7ABH_6 Splicing factor 3B subunit 1 (chains u)
MAKIAKTHEDIEAQIREIQGKKAALDEAQGVGLDSTGYYDQEIYGGSDSRFAGYVTSIAA
TELEDDDDDYSSSTSLLGQKKPGYHAPVALLNDIPQSTEQYDPFAEHRPPKIADREDEYK
KHRRTMIISPERLDPFADGGKTPDPKMNARTYMDVMREQHLTKEEREIRQQLAEKAKAGE
LKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAETPGHTPSLRWDETPGRAK
GSETPGATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRWDETPKTE
RDTPGHGSGWAETPRTDRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPI
GTPAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKVLPPPAG
YVPIRTPARKLTATPTPLGGMTGFHMQTEDRTMKSVNDQPSGNLPFLKPDDIQYFDKLLV
DVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLM
SPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNL
AKAAGLATMISTMRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQA
RHTGIKIVQQIAILMGCAILPHLRSLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYG
IESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSP
DEEMKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVEL
ANKVGAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAF
QEQTTEDSVMLNGFGTVVNALGKRVKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAV
VMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVIGMHKMTPPIKDLLPRL
TPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNT
FGYIAKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPE
LNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVY
GFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPCRMLQYCLQGLFHPARK
VRDVYWKIYNSIYIGSQDALIAHYPRIYNDDKNTYIRYELDYIL
Sequence of entity 7 (T), FASTA
>7ABH_7 Splicing factor 3B subunit 2 (chains T)
MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF
Sequence of entity 8 (E), FASTA
>7ABH_8 Splicing factor 3B subunit 3 (chains E)
MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFG
VIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQF
LAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFENP
MFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG
GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFF
FLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQ
IAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANEDT
PQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN
ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPG
KKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQ
RSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERGSI
GFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSW
LSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFP
LQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAA
AFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTG
EDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVL
IGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQ
LIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRG
LLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDF
FQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRT
PPEVSKKLEDIRTRYAF
Sequence of entity 9 (w), FASTA
>7ABH_9 Splicing factor 3B subunit 4 (chains w)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ
Sequence of entity 10 (x), FASTA
>7ABH_10 Splicing factor 3B subunit 5 (chains x)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN
Sequence of entity 11 (z), FASTA
>7ABH_11 Splicing factor 3B subunit 6 (chains z)
MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA
YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN
TDPPK
Sequence of entity 12 (0), FASTA
>7ABH_12 Smad nuclear-interacting protein 1 (chains 0)
MKAVKSERERGSRRRHRDGDVVLPAGVVVKQERLSPEVAPPAHRRPDHSGGSPSPPTSEP
ARSGHRGNRARGVSRSPPKKKNKASGRRSKSPRSKRNRSPHHSTVKVKQEREDHPRRGRE
DRQHREPSEQEHRRARNSDRDRHRGHSHQRRTSNERPGSGQGQGRDRDTQNLQAQEEERE
FYNARRREHRQRNDVGGGGSESQELVPRPGGNNKEKEVPAKEKPSFELSGALLEDTNTFR
GVVIKYSEPPEARIPKKRWRLYPFKNDEVLPVMYIHRQSAYLLGRHRRIADIPIDHPSCS
KQHAVFQYRLVEYTRADGTVGRRVKPYIIDLGSGNGTFLNNKRIEPQRYYELKEKDVLKF
GFSSREYVLLHESSDTSEIDRKDDEDEEEEEEVSDS

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 Q99459 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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