8Q7N: Human spliceosomal B complex protomer

cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region). Determined by electron microscopy at 3.1 Å resolution. Released 24 Jan 2024.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
21
Atoms
55,463
Mol. weight
1427.48 kDa
Released
24 Jan 2024

Explore 8Q7N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q7N contains 325 α-helices and 198 β-strands across 17 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 7: 4 helices, 1 β-strand

ElementResiduesLengthSheet
β-strand41211
α-helix422-43110
α-helix436-44914
α-helix452-4543
α-helix459-47113
Chain A: 108 helices, 76 β-strands
ElementResiduesLengthSheet
α-helix63-7311
α-helix79-813
α-helix85-906
α-helix91-933
α-helix95-10410
α-helix106-1083
β-strand115-121735
β-strand127-129335
β-strand134-135236
α-helix137-15721
α-helix163-1653
α-helix173-1775
α-helix178-1825
α-helix189-1913
α-helix201-2044
β-strand220137
β-strand227-229337
α-helix232-24110
α-helix252-2554
α-helix260-2689
α-helix276-2783
β-strand294138
α-helix299-3013
α-helix310-3156
α-helix317-3204
α-helix329-3313
α-helix334-3374
α-helix357-3593
β-strand37913
α-helix398-4058
β-strand415-417337
β-strand419-420236
α-helix421-4233
α-helix428-4314
α-helix434-4352
α-helix441-46020
α-helix463-4664
α-helix472-4776
β-strand482-488735
α-helix489-51022
β-strand516-518339
β-strand524-526339
α-helix529-5313
α-helix532-5376
α-helix542-56524
α-helix571-58313
α-helix585-5884
α-helix591-5933
α-helix596-5983
α-helix599-61618
α-helix631-65929
α-helix681-69515
α-helix706-72116
α-helix733-76230
α-helix769-79729
α-helix804-82017
α-helix822-8243
β-strand825140
α-helix826-8294
α-helix835-84713
α-helix858-87215
α-helix874-88714
α-helix892-8932
β-strand894-900741
β-strand905-910641
α-helix913-93220
α-helix948-96013
β-strand973-980842
β-strand981143
α-helix990-9978
β-strand1001140
α-helix1003-101311
β-strand1016-1019441
β-strand1022-1025441
α-helix1037-106226
α-helix1077-10804
β-strand1085-1091742
β-strand1094-1101842
α-helix1103-111614
β-strand1142138
α-helix1145-115915
β-strand1168143
β-strand1174-1178542
β-strand1185-1188444
β-strand1192145
β-strand1193-1198644
β-strand1213-1217544
β-strand1224-1229644
β-strand1232145
α-helix1234-124916
α-helix1256-127419
α-helix1277-12804
α-helix1282-130322
α-helix1314-13174
α-helix1320-13223
β-strand1334-1335246
β-strand1341-1346647
β-strand1349-1354647
α-helix1360-13623
β-strand1363-1364246
α-helix1365-13673
α-helix1369-13713
α-helix1375-139824
β-strand1403133
α-helix1419-14235
α-helix1436-14427
α-helix1443-14453
α-helix1468-147710
α-helix1480-14856
α-helix1490-14934
β-strand1501-1504423
α-helix1508-15125
α-helix1513-15153
α-helix1520-15245
α-helix1529-15379
α-helix1539-15424
β-strand1553-1554248
β-strand1561-1562248
α-helix1567-157610
α-helix1581-159919
β-strand1606-1611649
β-strand1629-16391149
α-helix1640-16423
β-strand1643-1644249
β-strand1655-16671349
α-helix1676-168813
β-strand1700-1706749
β-strand1711-1716649
α-helix1722-173514
α-helix1738-175114
β-strand1753-1755323
α-helix1759-17613
β-strand1762-1763250
α-helix1769-17724
β-strand1777-1778251
β-strand1779-1781352
β-strand1787-1792653
β-strand1798-1803653
β-strand1805-1810652
β-strand1818-1822552
α-helix1824-18274
α-helix1834-184916
β-strand1860-1862351
α-helix1866-18683
α-helix1869-18757
β-strand1883-1885351
β-strand1886-1887250
α-helix1895-18984
α-helix1900-19067
β-strand1914-1916352
α-helix1923-19253
α-helix1929-194517
α-helix1949-19535
α-helix1973-199523
α-helix1999-20013
α-helix2004-20129
β-strand2040-2041218
β-strand2042-2046520
β-strand2054-2058520
α-helix2073-20808
α-helix2084-20863
β-strand2091-2092254
β-strand2104-2107455
α-helix2108-21169
β-strand2124-2129654
β-strand2140-2141255
β-strand2144-2146354
β-strand2150156
β-strand2151-2152257
β-strand2157-2158257
α-helix2163-21642
β-strand2176-2180554
α-helix2190-220213
β-strand2212-2218754
β-strand2223-2230854
α-helix2232-22409
α-helix2253-22553
β-strand2256-2259454
β-strand2261-2264455
β-strand2270-2274554
β-strand2280156
β-strand2296-2298354
α-helix2300-23034
α-helix2311-23155
Chain C: 39 helices, 38 β-strands
ElementResiduesLengthSheet
α-helix116-1249
α-helix126-1283
β-strand129-13682
α-helix142-15312
α-helix172-1776
β-strand184-19182
β-strand197-20482
α-helix209-2113
α-helix212-2198
β-strand224-23072
α-helix237-24812
β-strand252-25872
α-helix262-2665
α-helix271-29121
β-strand307-31152
β-strand316-31832
α-helix320-33112
α-helix336-3405
β-strand348-35033
β-strand355-35733
α-helix368-3692
α-helix370-3745
α-helix375-38612
α-helix392-3987
α-helix405-4084
α-helix412-42413
α-helix428-4369
α-helix441-45212
β-strand45314
β-strand475-48395
β-strand490-49895
β-strand501-50226
β-strand506-51055
β-strand522-52655
β-strand530-53345
β-strand53412
β-strand538-54145
β-strand543-54426
β-strand549-55355
β-strand563-56645
β-strand57714
α-helix578-5825
β-strand588-59477
α-helix597-5993
α-helix600-61314
β-strand618-62147
β-strand627-63157
α-helix634-6429
α-helix643-6497
β-strand653-65537
α-helix656-6583
β-strand659-66027
β-strand663-66648
β-strand674-67749
β-strand684-69079
α-helix691-6933
α-helix696-7016
α-helix711-72010
α-helix726-7305
β-strand732-73659
β-strand743-74759
α-helix756-7605
α-helix763-77614
β-strand78418
β-strand787-79599
α-helix805-82117
β-strand825-838148
α-helix840-8423
α-helix843-85210
β-strand856-86278
α-helix8631
β-strand869-87688
α-helix877-8793
α-helix883-8908
β-strand896-906118
α-helix9071
α-helix926-94116
Chain D: 4 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand7-8210
α-helix11-199
β-strand25-31710
α-helix36-4914
β-strand56-61610
α-helix69-735
β-strand79-84610
β-strand89110
β-strand91-93311
β-strand102110
α-helix109-12416
β-strand129-131311
Chain F: 6 helices, 29 β-strands
ElementResiduesLengthSheet
α-helix82-9615
α-helix105-11410
α-helix126-13914
α-helix144-1518
β-strand168-169225
α-helix172-20130
α-helix204-21916
β-strand221-228826
β-strand234-239627
β-strand245-250627
β-strand255-259527
β-strand265-269527
β-strand276-281628
β-strand296-300528
β-strand305-308428
β-strand317-319328
β-strand326-331629
β-strand337-342629
β-strand347-351529
β-strand357-361529
β-strand368-373630
β-strand379-384630
β-strand389-393530
β-strand398-402530
β-strand410-415631
β-strand421-426631
β-strand431-435531
β-strand440-445631
β-strand452-457632
β-strand464-469632
β-strand473-478632
β-strand484-489632
β-strand495-500626
β-strand506-511626
β-strand515-521726
Chain I: 14 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix5-62
α-helix12-143
α-helix17-204
α-helix23-308
α-helix33-375
α-helix44-529
β-strand57112
β-strand60-61213
β-strand66-67213
α-helix69-8012
α-helix84-929
α-helix97-11014
α-helix113-1208
α-helix121-1255
β-strand129-133512
β-strand139-143512
α-helix144-15310
β-strand156-157214
β-strand160-161214
α-helix162-1676
α-helix168-1736
Chain J: 13 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix389-3946
β-strand417-418225
β-strand43711
α-helix442-46524
α-helix470-4745
α-helix481-4844
α-helix486-4916
α-helix493-51826
α-helix519-5213
α-helix522-53413
β-strand541-548858
α-helix554-56613
β-strand570-575658
β-strand580-586758
α-helix588-5969
α-helix597-6015
β-strand630-638958
β-strand647-650458
α-helix654-66411
α-helix667-68216
Chain K: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix272-31342
α-helix334-3363
α-helix339-3413
α-helix354-3574

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
U5 snRNA5RNA117Homo sapiens
U6 snRNA6RNA106Homo sapiens
Splicing factor 3A subunit 17protein793Homo sapiensQ15459 (AlphaFold model)
116 kDa U5 small nuclear ribonucleoprotein componentCprotein972Homo sapiensQ15029 (AlphaFold model)
Thioredoxin-like protein 4ADprotein142Homo sapiensP83876 (AlphaFold model)
Pre-mRNA-splicing factor 38AIprotein312Homo sapiensQ8NAV1 (AlphaFold model)
Microfibrillar-associated protein 1Kprotein439Homo sapiensP55081
NHP2-like protein 1, N-terminally processedMprotein128Homo sapiensP55769
Protein BUD31 homologQprotein144Homo sapiensP41223
WW domain-binding protein 4Xprotein376Homo sapiensO75554
MINX pre-mRNAZRNA347Homo sapiens
Zinc finger matrin-type protein 2rprotein199Homo sapiensQ96NC0

9 more molecules are not listed.

Sequence of entity 1 (5), FASTA
>8Q7N_1 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA
Sequence of entity 2 (6), FASTA
>8Q7N_2 U6 snRNA (chains 6)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUU
Sequence of entity 3 (7), FASTA
>8Q7N_3 Splicing factor 3A subunit 1 (chains 7)
MPAGPVQAVPPPPPVPTEPKQPTEEEASSKEDSAPSKPVVGIIYPPPEVRNIVDKTASFV
ARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEFKEGKAQEPSAAIPKVMQQQ
QQTTQQQLPQKVQAQVIQETIVPKEPPPEFEFIADPPSISAFDLDVVKLTAQFVARNGRQ
FLTQLMQKEQRNYQFDFLRPQHSLFNYFTKLVEQYTKILIPPKGLFSKLKKEAENPREVL
DQVCYRVEWAKFQERERKKEEEEKEKERVAYAQIDWHDFVVVETVDFQPNEQGNFPPPTT
PEELGARILIQERYEKFGESEEVEMEVESDEEDDKQEKAEEPPSQLDQDTQVQDMDEGSD
DEEEGQKVPPPPETPMPPPLPPTPDQVIVRKDYDPKASKPLPPAPAPDEYLVSPITGEKI
PASKMQEHMRIGLLDPRWLEQRDRSIREKQSDDEVYAPGLDIESSLKQLAERRTDIFGVE
ETAIGKKIGEEEIQKPEEKVTWDGHSGSMARTQQAAQANITLQEQIEAIHKAKGLVPEDD
TKEKIGPSKPNEIPQQPPPPSSATNIPSSAPPITSVPRPPTMPPPVRTTVVSAVPVMPRP
PMASVVRLPPGSVIAPMPPIIHAPRINVVPMPPSAPPIMAPRPPPMIVPTAFVPAPPVAP
VPAPAPMPPVHPPPPMEDEPTSKKLKTEDSLMPEEEFLRRNKGPVSIKVQVPNMQDKTEW
KLNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAV
IHLALKERGGRKK
Sequence of entity 4 (C), FASTA
>8Q7N_4 116 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 5 (D), FASTA
>8Q7N_5 Thioredoxin-like protein 4A (chains D)
MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYL
VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVY
RGARKGRGLVVSPKDYSTKYRY
Sequence of entity 6 (I), FASTA
>8Q7N_6 Pre-mRNA-splicing factor 38A (chains I)
MANRTVKDAHSIHGTNPQYLVEKIIRTRIYESKYWKEECFGLTAELVVDKAMELRFVGGV
YGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYL
EPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVLEEAEQLEPR
VSALEEDMDDVESSEEEEEEDEKLERVPSPDHRRRSYRDLDKPRRSPTLRYRRSRSRSPR
RRSRSPKRRSPSPRRERHRSKSPRRHRSRSRDRRHRSRSKSPGHHRSHRHRSHSKSPERS
KKSHKKSRRGNE
Sequence of entity 7 (K), FASTA
>8Q7N_7 Microfibrillar-associated protein 1 (chains K)
MSVPSALMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEF
QFIKKAKEQEAEPEEQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEV
EGDAWRMEREDSSEEEEEEIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESE
SESEYEEYTDSEDEMEPRLKPVFIRKKDRVTVQEREAEALKQKELEQEAKRMAEERRKYT
LKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWKVRELKRIKRDREDREALEKE
KAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFFMDEDEEVYKRDF
SAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQK
AAGVRDVFERPSAKKRKTT
Sequence of entity 8 (M), FASTA
>8Q7N_8 NHP2-like protein 1, N-terminally processed (chains M)
MTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADA
EPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQ
QSIERLLV
Sequence of entity 9 (Q), FASTA
>8Q7N_9 Protein BUD31 homolog (chains Q)
MPKVKRSRKAPPDGWELIEPTLDELDQKMREAETEPHEGKRKVESLWPIFRIHHQKTRYI
FDLFYKRKAISRELYEYCIKEGYADKNLIAKWKKQGYENLCCLRCIQTRDTNFGTNCICR
VPKSKLEVGRIIECTHCGCRGCSG
Sequence of entity 10 (X), FASTA
>8Q7N_10 WW domain-binding protein 4 (chains X)
MADYWKSQPKKFCDYCKCWIADNRPSVEFHERGKNHKENVAKRISEIKQKSLDKAKEEEK
ASKEFAAMEAAALKAYQEDLKRLGLESEILEPSITPVTSTIPPTSTSNQQKEKKEKKKRK
KDPSKGRWVEGITSEGYHYYYDLISGASQWEKPEGFQGDLKKTAVKTVWVEGLSEDGFTY
YYNTETGESRWEKPDDFIPHTSDLPSSKVNENSLGTLDESKSSDSHSDSDGEQEAEEGGV
STETEKPKIKFKEKNKNSDGGSDPETQKEKSIQKQNSLGSNEEKSKTLKKSNPYGEWQEI
KQEVESHEEVDLELPSTENEYVSTSEADGGGEPKVVFKEKTVTSLGVMADGVAPVFKKRR
TENGKSRNLRQRGDDQ
Sequence of entity 11 (Z), FASTA
>8Q7N_11 MINX pre-mRNA (chains Z)
GGUACCUAAUACGACUCACUAUAGGGAGACGGAAUUCGAGCUCGCCCACUCUUGGAUCGG
AAACCCGUCGGCCUCCGAACGGUAAGAGCCUAGCAUGUAGAACUGGUUACCUGCAGCCCA
AGCUUGCUGCACGUCUAGGGCGCAGUAGUCCAGGGUUUCCUUGAUGAUGUCAUACUUAUC
CUGUCCCUUUUUUUUCCACAGCUCGCGGUUGAGGACAAACUCUUCGCGGUCUUUCCAGUG
GGGAUCCAAUAUCCGUACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGGG
UACGACUAGUAGAUCUCGUACACCAUCAGGGUACGGAAUUCUCUAGA
Sequence of entity 12 (r), FASTA
>8Q7N_12 Zinc finger matrin-type protein 2 (chains r)
MASGSGTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPVQPVKRELLRHRDYKVDLES
KLGKTIVITKTTPQSEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTLD
QVKKRFEVNKKKMEEKQKDYDFEERMKELREEEEKAKAYKKEKQKEKKRRAEEDLTFEED
DEMAAVMGFSGFGSTKKSY

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 Q15459 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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