8R0A: Cross-exon pre-B+5'ss complex
Cryo-EM structure of the cross-exon pre-B+5'ss complex. Determined by electron microscopy at 5.8 Å resolution. Released 22 May 2024.
- Method
- Electron microscopy
- Resolution
- 5.8 Å
- Organism
- Homo sapiens
- Chains
- 62
- Atoms
- 80,982
- Mol. weight
- 2806.15 kDa
- Released
- 22 May 2024
Explore 8R0A in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8R0A contains 595 α-helices and 625 β-strands across 56 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 21: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| β-strand | 13-19 | 7 | 1 |
| β-strand | 24-32 | 9 | 1 |
| β-strand | 38-46 | 9 | 1 |
| β-strand | 53-60 | 8 | 1 |
| β-strand | 65-70 | 6 | 1 |
Chain 22: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-26 | 13 | |
| α-helix | 30-35 | 6 | |
| β-strand | 41-45 | 5 | 1 |
| β-strand | 50-58 | 9 | 1 |
| β-strand | 65-74 | 10 | 1 |
| β-strand | 76 | 1 | 2 |
| β-strand | 90 | 1 | 2 |
| β-strand | 93-101 | 9 | 1 |
| β-strand | 108-110 | 3 | 1 |
Chain 23: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| β-strand | 17-21 | 5 | 1 |
| β-strand | 27-35 | 9 | 1 |
| β-strand | 41-48 | 8 | 1 |
| β-strand | 56-58 | 3 | 1 |
| β-strand | 61-63 | 3 | 1 |
| β-strand | 70-73 | 4 | 1 |
| α-helix | 75-77 | 3 | |
Chain 2A: 6 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| β-strand | 13-16 | 4 | 52 |
| β-strand | 22-25 | 4 | 52 |
| α-helix | 37-40 | 4 | |
| β-strand | 46-48 | 3 | 52 |
| β-strand | 56-57 | 2 | 53 |
| β-strand | 68-70 | 3 | 52 |
| β-strand | 78-79 | 2 | 53 |
| β-strand | 92-94 | 3 | 52 |
| α-helix | 103-106 | 4 | |
| α-helix | 108-111 | 4 | |
| β-strand | 117-119 | 3 | 52 |
| α-helix | 131-138 | 8 | |
| β-strand | 144-145 | 2 | 52 |
| β-strand | 149 | 1 | 52 |
| α-helix | 152-160 | 9 | |
Chain 2b: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-21 | 6 | 1 |
| β-strand | 26-34 | 9 | 1 |
| β-strand | 40-51 | 12 | 1 |
| α-helix | 58-60 | 3 | |
| β-strand | 61-72 | 12 | 1 |
| β-strand | 77-84 | 8 | 1 |
Chain 2B: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-12 | 5 | 13 |
| α-helix | 20-30 | 11 | |
| β-strand | 37-43 | 7 | 13 |
| β-strand | 51-56 | 6 | 13 |
| α-helix | 59-68 | 10 | |
| β-strand | 72-74 | 3 | 14 |
| β-strand | 77-79 | 3 | 14 |
| β-strand | 80-83 | 4 | 13 |
| α-helix | 89-93 | 5 | |
Chain 2e: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-27 | 11 | |
| β-strand | 30-35 | 6 | 1 |
| β-strand | 38-49 | 12 | 1 |
| β-strand | 56-65 | 10 | 1 |
| β-strand | 71-79 | 9 | 1 |
| β-strand | 84-89 | 6 | 1 |
Chain 2f: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| β-strand | 15 | 1 | 1 |
| β-strand | 18-23 | 6 | 1 |
| β-strand | 27-36 | 10 | 1 |
| β-strand | 42-51 | 10 | 1 |
| β-strand | 54-64 | 11 | 1 |
| β-strand | 69-74 | 6 | 1 |
48 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| U5 snRNA | 5 | RNA | 117 | Homo sapiens | |
| 116 kDa U5 small nuclear ribonucleoprotein component | C | protein | 972 | Homo sapiens | Q15029 (AlphaFold model) |
| Thioredoxin-like protein 4A | D | protein | 142 | Homo sapiens | P83876 (AlphaFold model) |
| U5 small nuclear ribonucleoprotein 40 kDa protein | E | protein | 357 | Homo sapiens | Q96DI7 (AlphaFold model) |
| U4/U6 small nuclear ribonucleoprotein Prp4 | F | protein | 522 | Homo sapiens | O43172 (AlphaFold model) |
| NHP2-like protein 1, N-terminally processed | M | protein | 128 | Homo sapiens | P55769 |
| RNA-binding protein 42 | R | protein | 480 | Homo sapiens | Q9BTD8 |
| Ubiquitin carboxyl-terminal hydrolase 39 | U | protein | 565 | Homo sapiens | Q53GS9 |
| U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein | X | protein | 155 | Homo sapiens | Q8WVK2 |
| pre-mRNA | Z | RNA | 347 | Homo sapiens | |
| 5'ss oligo | z | RNA | 11 | Homo sapiens | |
| Pre-mRNA-processing-splicing factor 8 | A | protein | 2335 | Homo sapiens | Q6P2Q9 |
36 more molecules are not listed.
Sequence of entity 1 (5), FASTA
>8R0A_1 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA
Sequence of entity 2 (C), FASTA
>8R0A_2 116 kDa U5 small nuclear ribonucleoprotein component (chains C)
MDTDLYDEFGNYIGPELDSDEDDDELGRETKDLDEMDDDDDDDDVGDHDDDHPGMEVVLH
EDKKYYPTAEEVYGPEVETIVQEEDTQPLTEPIIKPVKTKKFTLMEQTLPVTVYEMDFLA
DLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHPEIRKRYDQDLCYTDILFTEQERGVG
IKSTPVTVVLPDTKGKSYLFNIMDTPGHVNFSDEVTAGLRISDGVVLFIDAAEGVMLNTE
RLIKHAVQERLAVTVCINKIDRLILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLIL
SPLLGNVCFSSSQYSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRKFTKKA
PTSSSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTKEELKLNIRPLLRLVC
KKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK
MYSTDDGVQFHAFGRVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGRLWISVARYHIE
VNRVPAGNWVLIEGVDQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSEL
PKMLDGLRKVNKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVV
TFCETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVVQITWNRKKLGEFFQT
KYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVDKALLGSVKDSIVQGFQWGTREGPLC
DELIRNVKFKILDAVVAQEPLHRGGGQIIPTARRVVYSAFLMATPRLMEPYYFVEVQAPA
DCVSAVYTVLARRRGHVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSV
FHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDPMLLE
LAKQDVVLNYPM
Sequence of entity 3 (D), FASTA
>8R0A_3 Thioredoxin-like protein 4A (chains D)
MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYL
VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVY
RGARKGRGLVVSPKDYSTKYRY
Sequence of entity 4 (E), FASTA
>8R0A_4 U5 small nuclear ribonucleoprotein 40 kDa protein (chains E)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ
Sequence of entity 5 (F), FASTA
>8R0A_5 U4/U6 small nuclear ribonucleoprotein Prp4 (chains F)
MASSRASSTQATKTKAPDDLVAPVVKKPHIYYGSLEEKERERLAKGESGILGKDGLKAGI
EAGNINITSGEVFEIEEHISERQAEVLAEFERRKRARQINVSTDDSEVKACLRALGEPIT
LFGEGPAERRERLRNILSVVGTDALKKTKKDDEKSKKSKEEYQQTWYHEGPNSLKVARLW
IANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPISYCHFS
PNSKMLATACWSGLCKLWSVPDCNLLHTLRGHNTNVGAIVFHPKSTVSLDPKDVNLASCA
ADGSVKLWSLDSDEPVADIEGHTVRVARVMWHPSGRFLGTTCYDRSWRLWDLEAQEEILH
QEGHSMGVYDIAFHQDGSLAGTGGLDAFGRVWDLRTGRCIMFLEGHLKEIYGINFSPNGY
HIATGSGDNTCKVWDLRQRRCVYTIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWTHP
GWSPLKTLAGHEGKVMGLDISSDGQLIATCSYDRTFKLWMAE
Sequence of entity 6 (M), FASTA
>8R0A_6 NHP2-like protein 1, N-terminally processed (chains M)
MTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADA
EPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQ
QSIERLLV
Sequence of entity 7 (R), FASTA
>8R0A_7 RNA-binding protein 42 (chains R)
MAGAGPAPGLPGAGGPVVPGPGAGIPGKSGEERLKEMEAEMALFEQEVLGAPVPGIPTAV
PAVPTVPTVPTVEAMQVPAAPVIRPIIATNTYQQVQQTLEARAAAAATVVPPMVGGPPFV
GPVGFGPGDRSHLDSPEAREAMFLRRAAVAPQRAPILRPAFVPHVLQRADSALSSAAAGP
RPMALRPPHQALVGPPLPGPPGPPMMLPPMARAPGPPLGSMAALRPPLEEPAAPRELGLG
LGLGLKEKEEAVVAAAAGLEEASAAVAVGAGGAPAGPAVIGPSLPLALAMPLPEPEPLPL
PLEVVRGLLPPLRIPELLSLRPRPRPPRPEPPPGLMALEVPEPLGEDKKKGKPEKLKRCI
RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGK
TKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKLRKSMWKDRNLDVVRKKQKEKKKLGLR
Sequence of entity 8 (U), FASTA
>8R0A_8 Ubiquitin carboxyl-terminal hydrolase 39 (chains U)
MSGRSKRESRGSTRGKRESESRGSSGRVKRERDREREPEAASSRGSPVRVKREFEPASAR
EAPASVVPFVRVKREREVDEDSEPEREVRAKNGRVDSEDRRSRHCPYLDTINRSVLDFDF
EKLCSISLSHINAYACLVCGKYFQGRGLKSHAYIHSVQFSHHVFLNLHTLKFYCLPDNYE
IIDSSLEDITYVLKPTFTKQQIANLDKQAKLSRAYDGTTYLPGIVGLNNIKANDYANAVL
QALSNVPPLRNYFLEEDNYKNIKRPPGDIMFLLVQRFGELMRKLWNPRNFKAHVSPHEML
QAVVLCSKKTFQITKQGDGVDFLSWFLNALHSALGGTKKKKKTIVTDVFQGSMRIFTKKL
PHPDLPAEEKEQLLHNDEYQETMVESTFMYLTLDLPTAPLYKDEKEQLIIPQVPLFNILA
KFNGITEKEYKTYKENFLKRFQLTKLPPYLIFCIKRFTKNNFFVEKNPTIVNFPITNVDL
REYLSEEVQAVHKNTTYDLIANIVHDGKPSEGSYRIHVLHHGTGKWYELQDLQVTDILPQ
MITLSEAYIQIWKRRDNDETNQQGA
Sequence of entity 9 (X), FASTA
>8R0A_9 U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein (chains X)
MGRSRSRSPRRERRRSRSTSRERERRRRERSRSRERDRRRSRSRSPHRRRSRSPRRHRST
SPSPSRLKERRDEEKKETKETKSKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGKKV
DGSVNAYAINVSQKRKYRQYMNRKGGFNRPLDFIA
Sequence of entity 10 (Z), FASTA
>8R0A_10 pre-mRNA (chains Z)
GGUACCUAAUACGACUCACUAUAGGGAGACGGAAUUCGAGCUCGCCCACUCUUGGAUCGG
AAACCCGUCGGCCUCCGAACGGUAAGAGCCUAGCAUGUAGAACUGGUUACCUGCAGCCCA
AGCUUGCUGCACGUCUAGGGCGCAGUAGUCCAGGGUUUCCUUGAUGAUGUCAUACUUAUC
CUGUCCCUUUUUUUUCCACAGCUCGCGGUUGAGGACAAACUCUUCGCGGUCUUUCCAGUG
GGGAUCCAAUAUCCGUACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGGG
UACGACUAGUAGAUCUCGUACACCAUCAGGGUACGGAAUUCUCUAGA
Sequence of entity 11 (z), FASTA
>8R0A_11 5'ss oligo (chains z)
AAGGUAAGUAU
Sequence of entity 12 (A), FASTA
>8R0A_12 Pre-mRNA-processing-splicing factor 8 (chains A)
MAGVFPYRGPGNPVPGPLAPLPDYMSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKED
MPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLY
HITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDYAD
NILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYR
LANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDIN
KIIIRQPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPIS
HRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRR
ALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKATK
FFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRF
GNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMR
QIRMCKDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQF
EGRHSKGVAKTVTKQRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCW
KANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLT
RLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLI
LALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMD
LYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGIN
NLQDVWETSEGECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYK
DMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATE
AAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARM
RLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFECRILPKC
RTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIV
NKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPK
ELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFI
DSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRT
DFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEG
LFWEKASGFEESMKWKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGI
FMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSY
KMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYA
RAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPAL
YVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTT
KPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQ
IIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLY
DDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVE
VQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEISAPSQQRQQIAEIEKQTKEQSQLT
ATQTRTVNKHGDEIITSTTSNYETQTFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKET
GYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLP
GQLPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTP
GSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWN
YNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA
Primary citation
Structural insights into the cross-exon to cross-intron spliceosome switch. Zhang, Z., Kumar, V., Dybkov, O. et al. Nature (2024) 630:1012-1019. DOI 10.1038/s41586-024-07458-1 · PubMed
Other PDB entries of the same protein (UniProt Q15029 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
- 8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
- 8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
- 8C6J 2.8 Å, Human spliceosomal PM5 C* complex
- 6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
- 7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
- 6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
- 6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
- 9XTT 2.92 Å, Human minor spliceosome branching-completed C complex (after step-I)
- 6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
- 8I0R 3.0 Å, The cryo-EM structure of human Bact-I complex
- 8I0T 3.0 Å, The cryo-EM structure of human Bact-III complex
Browse structure collections
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