8CH6: Small nuclear ribonucleoprotein E

Name: PDB 8CH6: Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex).
Published: 2023-05-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: splicing

Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex). Determined by electron microscopy at 5.9 Å resolution. Released 10 May 2023.

Method: Electron microscopy
Resolution: 5.9 Å
Organisms: Homo sapiens, unidentified adenovirus
Chains: 59
Atoms: 119,058
Mol. weight: 3668.28 kDa
Ligands: ZN, IHP, GTP, MG
Released: 10 May 2023

Explore 8CH6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CH6 contains 686 α-helices and 675 β-strands across 55 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 1: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	1
β-strand	38-50	13	1
β-strand	56-65	10	1
β-strand	71-79	9	1
β-strand	84-90	7	1

Chain 2: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
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

Chain 3: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	11-13	3
β-strand	17-22	6	1
β-strand	27-35	9	1
β-strand	41-49	9	1
β-strand	55-63	9	1
β-strand	68-73	6	1

Chain 4: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	21-26	6
α-helix	30-38	9
β-strand	41-46	6	1
β-strand	50-56	7	1
β-strand	65-74	10	1
β-strand	94-101	8	1
β-strand	106-111	6	1

Chain 5: 2 helices, 6 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	53-54	2	1
β-strand	57-60	4	1
β-strand	65-69	5	1
α-helix	76-80	5

Chain 8: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	1
β-strand	26-31	6	1
β-strand	40-48	9	1
β-strand	64-72	9	1
β-strand	77-82	6	1

Chain 9: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	16-21	6	1
β-strand	25-33	9	1
β-strand	40-47	8	1
β-strand	55-62	8	1
β-strand	69-72	4	1

Chain a: 101 helices, 61 β-strands

Element	Residues	Length	Sheet
β-strand	60-61	2	78
α-helix	63-71	9
α-helix	82-84	3
α-helix	85-89	5
α-helix	95-103	9
α-helix	106-108	3
β-strand	115-121	7	78
β-strand	127-129	3	78
β-strand	134-135	2	79
α-helix	137-157	21
α-helix	163-165	3
α-helix	173-177	5
α-helix	178-181	4
α-helix	193-196	4
β-strand	220	1	80
β-strand	227-229	3	80
α-helix	232-241	10
α-helix	260-269	10
α-helix	295-297	3
α-helix	310-315	6
α-helix	317-320	4
α-helix	329-331	3
α-helix	334-336	3
α-helix	357-358	2
α-helix	396-405	10
β-strand	415-417	3	80
β-strand	419-420	2	79
α-helix	428-432	5
α-helix	441-459	19
α-helix	472-478	7
β-strand	482-488	7	78
α-helix	489-510	22
β-strand	516-518	3	81
β-strand	524-526	3	81
α-helix	532-537	6
α-helix	542-565	24
α-helix	571-583	13
α-helix	585-588	4
α-helix	596-598	3
α-helix	599-616	18
α-helix	631-660	30
α-helix	669-671	3
α-helix	674-676	3
α-helix	677-691	15
α-helix	706-721	16
α-helix	733-763	31
α-helix	769-797	29
α-helix	804-819	16
α-helix	823-825	3
α-helix	827-829	3
α-helix	835-847	13
α-helix	858-872	15
α-helix	874-886	13
β-strand	894-900	7	82
β-strand	905-910	6	82
α-helix	913-933	21
β-strand	940-941	2	83
α-helix	948-960	13
β-strand	974-979	6	83
α-helix	990-1000	11
α-helix	1003-1013	11
β-strand	1016-1019	4	82
β-strand	1022-1025	4	82
α-helix	1037-1053	17
α-helix	1055-1062	8
α-helix	1077-1081	5
β-strand	1085-1091	7	83
β-strand	1094-1100	7	83
α-helix	1103-1116	14
α-helix	1140-1141	2
α-helix	1144-1160	17
β-strand	1174-1178	5	83
β-strand	1185-1189	5	84
β-strand	1192-1198	7	84
β-strand	1213-1217	5	84
β-strand	1224-1232	9	84
α-helix	1234-1250	17
α-helix	1251-1253	3
α-helix	1256-1274	19
α-helix	1275-1278	4
α-helix	1282-1302	21
α-helix	1314-1317	4
β-strand	1319	1	85
α-helix	1320-1322	3
β-strand	1325	1	85
β-strand	1334-1337	4	86
α-helix	1340-1343	4
β-strand	1352-1355	4	86
α-helix	1365-1367	3
α-helix	1368-1370	3
α-helix	1373-1374	2
α-helix	1375-1399	25
β-strand	1402	1	39
α-helix	1405-1408	4
α-helix	1419-1423	5
α-helix	1429-1431	3
α-helix	1436-1446	11
α-helix	1450-1451	2
α-helix	1468-1476	9
α-helix	1481-1487	7
α-helix	1528-1537	10
α-helix	1539-1542	4
β-strand	1552-1554	3	87
α-helix	1555	1
β-strand	1561-1563	3	87
α-helix	1567-1576	10
α-helix	1581-1599	19
β-strand	1606-1611	6	88
α-helix	1616-1619	4
β-strand	1629-1639	11	88
α-helix	1640-1641	2
β-strand	1643-1644	2	88
β-strand	1655-1667	13	88
α-helix	1677-1687	11
β-strand	1700-1706	7	88
β-strand	1711-1716	6	88
α-helix	1723-1736	14
α-helix	1738-1751	14
β-strand	1755	1	104
α-helix	1767-1770	4
β-strand	1777	1	89
β-strand	1779-1781	3	90
β-strand	1789-1790	2	91
β-strand	1800-1801	2	91
α-helix	1803-1805	3
β-strand	1806-1811	6	90
β-strand	1816-1821	6	90
α-helix	1833-1837	5
α-helix	1838-1851	14
β-strand	1860-1862	3	89
α-helix	1869-1875	7
β-strand	1883-1885	3	89
α-helix	1893-1895	3
α-helix	1900-1907	8
β-strand	1915-1918	4	90
α-helix	1929-1945	17
α-helix	1947-1954	8
α-helix	1958-1960	3
β-strand	1966	1	90
α-helix	1969-1970	2
α-helix	1973-1995	23
α-helix	2004-2012	9
α-helix	2069-2075	7
α-helix	2077-2079	3
α-helix	2080-2088	9
β-strand	2090	1	92
β-strand	2104-2105	2	92
α-helix	2108-2117	10
β-strand	2125-2131	7	92
β-strand	2140-2146	7	92
β-strand	2151-2152	2	93
β-strand	2157-2158	2	93
β-strand	2173-2181	9	92
α-helix	2190-2202	13
β-strand	2212-2218	7	92
β-strand	2223-2227	5	92
β-strand	2228-2229	2	94
α-helix	2232-2240	9
β-strand	2257-2258	2	94
β-strand	2270-2274	5	92
β-strand	2296-2299	4	92
α-helix	2301-2303	3

47 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
Small nuclear ribonucleoprotein E	1, i	protein	92	Homo sapiens	P62304 (AlphaFold model)
Small nuclear ribonucleoprotein F	2, h	protein	86	Homo sapiens	P62306 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D3	3, j	protein	126	Homo sapiens	P62318 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D2	4, l	protein	118	Homo sapiens	P62316 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D1	5, k	protein	119	Homo sapiens	P62314
Small nuclear ribonucleoprotein-associated proteins B and B'	8, n	protein	240	Homo sapiens	P14678
Small nuclear ribonucleoprotein G	9, m	protein	76	Homo sapiens	P62308
Splicing factor 3B subunit 3	A	protein	1217	Homo sapiens	Q15393
Splicing factor 3B subunit 5	B	protein	86	Homo sapiens	Q9BWJ5
Splicing factor 3B subunit 1	C	protein	1304	Homo sapiens	O75533
PHD finger-like domain-containing protein 5A	D	protein	110	Homo sapiens	Q7RTV0
Splicing factor 3B subunit 2	E	protein	895	Homo sapiens	Q13435

37 more molecules are not listed.

Sequence of entity 1 (1, i), FASTA

>8CH6_1 Small nuclear ribonucleoprotein E (chains 1, i)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Sequence of entity 2 (2, h), FASTA

>8CH6_2 Small nuclear ribonucleoprotein F (chains 2, h)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE

Sequence of entity 3 (3, j), FASTA

>8CH6_3 Small nuclear ribonucleoprotein Sm D3 (chains 3, j)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR

Sequence of entity 4 (4, l), FASTA

>8CH6_4 Small nuclear ribonucleoprotein Sm D2 (chains 4, l)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Sequence of entity 5 (5, k), FASTA

>8CH6_5 Small nuclear ribonucleoprotein Sm D1 (chains 5, k)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Sequence of entity 6 (8, n), FASTA

>8CH6_6 Small nuclear ribonucleoprotein-associated proteins B and B' (chains 8, n)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP

Sequence of entity 7 (9, m), FASTA

>8CH6_7 Small nuclear ribonucleoprotein G (chains 9, m)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV

Sequence of entity 8 (A), FASTA

>8CH6_8 Splicing factor 3B subunit 3 (chains A)
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 (B), FASTA

>8CH6_9 Splicing factor 3B subunit 5 (chains B)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 10 (C), FASTA

>8CH6_10 Splicing factor 3B subunit 1 (chains C)
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 11 (D), FASTA

>8CH6_11 PHD finger-like domain-containing protein 5A (chains D)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR

Sequence of entity 12 (E), FASTA

>8CH6_12 Splicing factor 3B subunit 2 (chains E)
MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	7

Primary citation

Structural basis of catalytic activation in human splicing. Schmitzova, J., Cretu, C., Dienemann, C. et al. Nature (2023) 617:842-850. DOI 10.1038/s41586-023-06049-w · PubMed

Other PDB entries of the same protein (UniProt P62304 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
5XJL 2.5 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with…
7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
5XJU 2.58 Å, Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with…
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
8C6J 2.8 Å, Human spliceosomal PM5 C* complex
9NH5 2.82 Å, CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA…
9NH6 2.82 Å, cryo-EM structure of human U7 snrnp with methylated noncleavable H2A* substrate pre-mRNA…
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)

Browse structure collections

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