8QO9: Human spliceosomal B complex protomer
Cryo-EM structure of a human spliceosomal B complex protomer. Determined by electron microscopy at 5.29 Å resolution. Released 24 Jan 2024.
- Method
- Electron microscopy
- Resolution
- 5.29 Å
- Organism
- Homo sapiens
- Chains
- 71
- Atoms
- 87,322
- Mol. weight
- 3162.17 kDa
- Released
- 24 Jan 2024
Explore 8QO9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QO9 contains 642 α-helices and 679 β-strands across 66 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: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| β-strand | 13-19 | 7 | 4 |
| β-strand | 24-32 | 9 | 4 |
| α-helix | 37 | 1 | |
| β-strand | 38-46 | 9 | 4 |
| β-strand | 52-60 | 9 | 4 |
| β-strand | 65-69 | 5 | 4 |
| α-helix | 76-79 | 4 | |
Chain 22: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-26 | 13 | |
| α-helix | 30-35 | 6 | |
| β-strand | 42-46 | 5 | 4 |
| β-strand | 51-58 | 8 | 4 |
| β-strand | 65-76 | 12 | 4 |
| β-strand | 90-101 | 12 | 4 |
| β-strand | 106-110 | 5 | 4 |
Chain 23: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| β-strand | 17-22 | 6 | 4 |
| β-strand | 27-35 | 9 | 4 |
| β-strand | 41-48 | 8 | 4 |
| β-strand | 56-58 | 3 | 4 |
| β-strand | 61-63 | 3 | 4 |
| α-helix | 65-67 | 3 | |
| β-strand | 68-73 | 6 | 4 |
| α-helix | 75-79 | 5 | |
Chain 2A: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| β-strand | 14-16 | 3 | 50 |
| β-strand | 22-25 | 4 | 50 |
| α-helix | 37-40 | 4 | |
| β-strand | 46-48 | 3 | 50 |
| β-strand | 56-57 | 2 | 51 |
| α-helix | 60-62 | 3 | |
| β-strand | 68-70 | 3 | 50 |
| β-strand | 78-79 | 2 | 51 |
| β-strand | 92-94 | 3 | 50 |
| α-helix | 104-111 | 8 | |
| β-strand | 117-119 | 3 | 50 |
| α-helix | 124-127 | 4 | |
| α-helix | 131-138 | 8 | |
| β-strand | 144-145 | 2 | 50 |
| β-strand | 148-149 | 2 | 50 |
| α-helix | 152-160 | 9 | |
Chain 2b: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-11 | 4 | |
| β-strand | 16-21 | 6 | 4 |
| β-strand | 26-34 | 9 | 4 |
| β-strand | 40-51 | 12 | 4 |
| α-helix | 58-60 | 3 | |
| β-strand | 61-72 | 12 | 4 |
| β-strand | 77-84 | 8 | 4 |
Chain 2B: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-12 | 5 | 152 |
| α-helix | 20-31 | 12 | |
| β-strand | 37-42 | 6 | 152 |
| β-strand | 52-56 | 5 | 152 |
| α-helix | 59-68 | 10 | |
| β-strand | 73-74 | 2 | 153 |
| β-strand | 77-78 | 2 | 153 |
| β-strand | 80-83 | 4 | 152 |
| α-helix | 89-93 | 5 | |
Chain 2e: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-27 | 11 | |
| β-strand | 30-35 | 6 | 4 |
| β-strand | 38-50 | 13 | 4 |
| β-strand | 56-65 | 10 | 4 |
| β-strand | 70-79 | 10 | 4 |
| α-helix | 81-83 | 3 | |
| β-strand | 84-89 | 6 | 4 |
Chain 2f: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| β-strand | 18-23 | 6 | 4 |
| β-strand | 27-36 | 10 | 4 |
| β-strand | 42-51 | 10 | 4 |
| β-strand | 54-64 | 11 | 4 |
| α-helix | 66-68 | 3 | |
| β-strand | 69-74 | 6 | 4 |
57 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 |
|---|
| Splicing factor 3B subunit 4 | B4 | protein | 424 | Homo sapiens | Q15427 (AlphaFold model) |
| Splicing factor 3A subunit 2 | 8, G | protein | 464 | Homo sapiens | Q15428 (AlphaFold model) |
| Splicing factor 3A subunit 3 | 9, H | protein | 501 | Homo sapiens | Q12874 (AlphaFold model) |
| Splicing factor 3B subunit 2 | B2 | protein | 895 | Homo sapiens | Q13435 (AlphaFold model) |
| Splicing factor 3B subunit 5 | B5 | protein | 86 | Homo sapiens | Q9BWJ5 |
| U2 snRNA | 2 | RNA | 188 | Homo sapiens | |
| Splicing factor 3B subunit 3 | B3 | protein | 1217 | Homo sapiens | Q15393 |
| PHD finger-like domain-containing protein 5A | BP | protein | 110 | Homo sapiens | Q7RTV0 |
| Splicing factor 3B subunit 1 | B1 | protein | 1304 | Homo sapiens | O75533 |
| Splicing factor 3B subunit 6 | B6 | protein | 125 | Homo sapiens | Q9Y3B4 |
| U6 snRNA-associated Sm-like protein LSm2 | 62 | protein | 95 | Homo sapiens | Q9Y333 |
| U6 snRNA-associated Sm-like protein LSm3 | 63 | protein | 102 | Homo sapiens | P62310 |
41 more molecules are not listed.
Sequence of entity 1 (B4), FASTA
>8QO9_1 Splicing factor 3B subunit 4 (chains B4)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ
Sequence of entity 2 (8, G), FASTA
>8QO9_2 Splicing factor 3A subunit 2 (chains 8, G)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN
Sequence of entity 3 (9, H), FASTA
>8QO9_3 Splicing factor 3A subunit 3 (chains 9, H)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL
Sequence of entity 4 (B2), FASTA
>8QO9_4 Splicing factor 3B subunit 2 (chains B2)
MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF
Sequence of entity 5 (B5), FASTA
>8QO9_5 Splicing factor 3B subunit 5 (chains B5)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN
Sequence of entity 6 (2), FASTA
>8QO9_6 U2 snRNA (chains 2)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUAGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC
Sequence of entity 7 (B3), FASTA
>8QO9_7 Splicing factor 3B subunit 3 (chains B3)
MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFG
VIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQF
LAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFENP
MFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG
GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFF
FLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQ
IAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANEDT
PQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN
ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPG
KKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQ
RSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERGSI
GFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSW
LSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFP
LQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAA
AFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTG
EDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVL
IGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQ
LIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRG
LLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDF
FQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRT
PPEVSKKLEDIRTRYAF
Sequence of entity 8 (BP), FASTA
>8QO9_8 PHD finger-like domain-containing protein 5A (chains BP)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR
Sequence of entity 9 (B1), FASTA
>8QO9_9 Splicing factor 3B subunit 1 (chains B1)
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 10 (B6), FASTA
>8QO9_10 Splicing factor 3B subunit 6 (chains B6)
MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA
YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN
TDPPK
Sequence of entity 11 (62), FASTA
>8QO9_11 U6 snRNA-associated Sm-like protein LSm2 (chains 62)
MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC
FIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ
Sequence of entity 12 (63), FASTA
>8QO9_12 U6 snRNA-associated Sm-like protein LSm3 (chains 63)
MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEET
VTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLRVG
Primary citation
Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. Zhang, Z., Kumar, V., Dybkov, O. et al. EMBO J (2024) 43:1065-1088. DOI 10.1038/s44318-024-00052-1 · PubMed
Other PDB entries of the same protein (UniProt Q15427 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
- 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.
- 8HK1 2.7 Å, The cryo-EM structure of human pre-17S U2 snRNP
- 7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
- 7VPX 3.0 Å, The cryo-EM structure of the human pre-A complex
- 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
- 8I0V 3.0 Å, The cryo-EM structure of human post-Bact complex
- 7ONB 3.1 Å, Structure of the U2 5' module of the A3'-SSA complex
- 7QTT 3.1 Å, Structural organization of a late activated human spliceosome (Baqr, core region)
- 8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.
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