8C6J: Human spliceosomal PM5 C* complex

Name: PDB 8C6J: Human spliceosomal PM5 C* complex
Published: 2023-07-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: splicing

Human spliceosomal PM5 C* complex. Determined by electron microscopy at 2.8 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 63
Atoms: 111,233
Mol. weight: 3425.22 kDa
Ligands: ZN, GTP, IHP, ATP
Released: 12 Jul 2023

Explore 8C6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C6J contains 801 α-helices and 636 β-strands across 58 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 4: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	17
α-helix	40-52	13
α-helix	62-74	13
α-helix	148-154	7
β-strand	155-157	3	17
α-helix	158-176	19

Chain 7: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	47-56	10
α-helix	63-73	11
β-strand	78-80	3	32
α-helix	88-98	11
β-strand	109-112	4	32
α-helix	116-129	14
β-strand	137-140	4	32
α-helix	146-155	10
β-strand	159-162	4	32
α-helix	164-172	9
β-strand	183-187	5	32
α-helix	189-192	4
α-helix	198-207	10
β-strand	213-217	5	32
α-helix	223-227	5
α-helix	228-231	4
α-helix	236	1
β-strand	237-239	3	32
α-helix	243-246	4
β-strand	251-253	3	33
β-strand	254-255	2	34
β-strand	256-257	2	35
α-helix	261-275	15
β-strand	279-283	5	33
α-helix	287-299	13
β-strand	305-306	2	33
α-helix	313-325	13
β-strand	330-333	4	33
α-helix	335-338	4
β-strand	346-351	6	33
α-helix	358-366	9
β-strand	375-379	5	33
β-strand	380-381	2	35
α-helix	386-396	11
β-strand	401-402	2	34

Chain 8: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	36
β-strand	73-78	6	37
α-helix	86-94	9
β-strand	101-106	6	37
α-helix	107	1
β-strand	113-121	9	37
α-helix	124-134	11
β-strand	137-138	2	38
β-strand	143-144	2	38
β-strand	145-148	4	37
β-strand	150	1	39
β-strand	151	1	36

Chain 9: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	10	44
β-strand	18-26	9	44
β-strand	31-37	7	44
β-strand	46-51	6	44
β-strand	52	1	39
α-helix	53	1
α-helix	54-67	14
α-helix	69-71	3
α-helix	78-80	3
β-strand	85-92	8	44
β-strand	95-101	7	44
α-helix	107-112	6
α-helix	116-140	25
α-helix	142-144	3

Chain a: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-26	11
α-helix	30-37	8
β-strand	41-45	5	136
β-strand	50-58	9	136
β-strand	65-74	10	136
β-strand	76	1	137
β-strand	90	1	137
β-strand	93-101	9	136
α-helix	103-105	3
β-strand	108-110	3	136

Chain A: 118 helices, 66 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
α-helix	47-49	3
α-helix	55-59	5
β-strand	60	1	47
α-helix	61-62	2
α-helix	63-73	11
α-helix	79-81	3
α-helix	85-90	6
α-helix	91-94	4
α-helix	95-104	10
α-helix	106-108	3
β-strand	115-121	7	47
β-strand	127-129	3	47
β-strand	134-135	2	48
α-helix	137-157	21
α-helix	163-165	3
α-helix	174-177	4
α-helix	178-181	4
α-helix	186-190	5
α-helix	201-204	4
β-strand	220	1	49
β-strand	227-229	3	49
α-helix	232-241	10
α-helix	260-269	10
α-helix	299-301	3
α-helix	310-315	6
α-helix	317-320	4
α-helix	329-331	3
α-helix	335-337	3
α-helix	357-358	2
β-strand	379	1	50
α-helix	398-405	8
β-strand	415-417	3	49
β-strand	419-420	2	48
α-helix	421-423	3
α-helix	428-432	5
α-helix	434-436	3
α-helix	441-460	20
α-helix	472-478	7
β-strand	482-488	7	47
α-helix	489-510	22
β-strand	516-518	3	51
β-strand	524-526	3	51
α-helix	529-531	3
α-helix	532-538	7
α-helix	542-566	25
α-helix	571-583	13
α-helix	585-588	4
α-helix	591-593	3
α-helix	596-598	3
α-helix	599-616	18
α-helix	631-661	31
α-helix	669-671	3
α-helix	674-676	3
α-helix	677-696	20
α-helix	706-721	16
α-helix	733-763	31
α-helix	769-796	28
α-helix	803-819	17
α-helix	822-827	6
β-strand	832	1	52
α-helix	835-847	13
α-helix	858-872	15
α-helix	874-887	14
β-strand	894-900	7	53
β-strand	905-910	6	53
α-helix	913-932	20
β-strand	940	1	54
α-helix	948-960	13
β-strand	973-980	8	54
β-strand	982	1	55
α-helix	990-997	8
α-helix	1003-1013	11
β-strand	1016-1019	4	53
β-strand	1022-1025	4	53
α-helix	1037-1053	17
α-helix	1055-1062	8
α-helix	1078-1081	4
β-strand	1085-1090	6	54
β-strand	1094-1101	8	54
α-helix	1103-1116	14
α-helix	1123-1125	3
α-helix	1136-1138	3
α-helix	1144-1160	17
β-strand	1167	1	55
β-strand	1174-1178	5	54
β-strand	1185-1189	5	56
β-strand	1192-1198	7	56
β-strand	1213-1217	5	56
β-strand	1224-1232	9	56
α-helix	1234-1250	17
α-helix	1256-1271	16
α-helix	1277-1280	4
α-helix	1282-1302	21
α-helix	1308-1310	3
α-helix	1313-1317	5
α-helix	1320-1322	3
α-helix	1334	1
β-strand	1335-1337	3	57
α-helix	1340-1343	4
β-strand	1352-1354	3	57
α-helix	1368-1371	4
α-helix	1375-1398	24
α-helix	1405-1407	3
α-helix	1419-1423	5
α-helix	1427-1430	4
α-helix	1436-1442	7
α-helix	1443-1445	3
α-helix	1468-1477	10
α-helix	1480-1485	6
α-helix	1490-1493	4
α-helix	1508-1513	6
α-helix	1528-1537	10
α-helix	1539-1542	4
β-strand	1552-1554	3	58
β-strand	1561-1563	3	58
α-helix	1567-1576	10
α-helix	1581-1599	19
β-strand	1606-1611	6	59
α-helix	1616-1620	5
β-strand	1626	1	60
β-strand	1629-1639	11	59
β-strand	1643-1644	2	59
β-strand	1655-1667	13	59
α-helix	1676-1688	13
β-strand	1694	1	60
β-strand	1700-1706	7	59
β-strand	1711-1716	6	59
α-helix	1722-1734	13
α-helix	1738-1751	14
β-strand	1758-1759	2	61
α-helix	1760-1762	3
β-strand	1763	1	62
α-helix	1768-1772	5
β-strand	1777-1781	5	63
β-strand	1787-1791	5	64
β-strand	1799-1803	5	64
β-strand	1805-1810	6	63
β-strand	1816-1822	7	63
α-helix	1824-1827	4
α-helix	1833-1851	19
α-helix	1854-1856	3
β-strand	1860-1863	4	63
α-helix	1866-1868	3
α-helix	1869-1875	7
α-helix	1876-1878	3
β-strand	1883-1885	3	63
β-strand	1887	1	62
α-helix	1894-1897	4
α-helix	1900-1907	8
β-strand	1913-1918	6	63
α-helix	1923-1925	3
α-helix	1929-1945	17
α-helix	1947-1954	8
α-helix	1973-1994	22
α-helix	1999-2001	3
α-helix	2004-2012	9
α-helix	2014-2016	3
α-helix	2073-2080	8
α-helix	2083-2088	6
β-strand	2090-2092	3	65
β-strand	2103-2107	5	65
α-helix	2108-2116	9
β-strand	2125-2131	7	65
α-helix	2132-2133	2
β-strand	2139-2146	8	65
β-strand	2150	1	66
β-strand	2151-2152	2	67
β-strand	2157-2158	2	67
α-helix	2163-2164	2
β-strand	2173-2181	9	65
α-helix	2190-2202	13
β-strand	2212-2217	6	65
β-strand	2223-2230	8	65
α-helix	2232-2240	9
α-helix	2253-2255	3
β-strand	2256-2259	4	65
β-strand	2261-2264	4	65
β-strand	2270-2274	5	65
β-strand	2280	1	66
β-strand	2296-2298	3	65
α-helix	2300-2303	4
α-helix	2311-2313	3
α-helix	2327-2329	3

Chain b: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	136
β-strand	26-34	9	136
β-strand	40-47	8	136
β-strand	66-72	7	136
α-helix	74-76	3
β-strand	77-82	6	136
α-helix	85-86	2

Chain B: 97 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	411-414	4
α-helix	416	1
α-helix	419-421	3
α-helix	429-431	3
β-strand	435-439	5	84
β-strand	442-446	5	84
α-helix	448-455	8
α-helix	461-462	2
β-strand	463	1	85
α-helix	464-466	3
α-helix	469-472	4
β-strand	480	1	85
α-helix	483-494	12
β-strand	499-502	4	86
α-helix	509-522	14
β-strand	537-541	5	86
α-helix	545-558	14
α-helix	560-562	3
β-strand	566-568	3	86
α-helix	573-582	10
β-strand	585-588	4	86
α-helix	590-599	10
β-strand	609-614	6	86
α-helix	617-621	5
α-helix	625-642	18
β-strand	647-652	6	86
α-helix	658-665	8
β-strand	673-675	3	86
α-helix	678-680	3
β-strand	687-692	6	84
α-helix	697-714	18
β-strand	721-725	5	84
α-helix	728-744	17
α-helix	749-753	5
α-helix	761-766	6
α-helix	774-780	7
β-strand	782-785	4	84
α-helix	791-802	12
β-strand	808-812	5	84
α-helix	814-818	5
β-strand	823	1	87
β-strand	825-828	4	84
β-strand	832-835	4	88
β-strand	840-843	4	88
α-helix	844-845	2
α-helix	846-853	8
β-strand	856	1	87
β-strand	867-872	6	84
α-helix	873-875	3
α-helix	876-883	8
α-helix	897-907	11
β-strand	912	1	89
α-helix	913-921	9
α-helix	924-931	8
α-helix	934-936	3
α-helix	940-945	6
α-helix	950-966	17
β-strand	970-972	3	90
β-strand	978	1	89
β-strand	979-981	3	90
α-helix	983-991	9
α-helix	995-1004	10
α-helix	1011-1019	9
α-helix	1022-1024	3
α-helix	1032-1034	3
α-helix	1035-1043	9
α-helix	1055-1068	14
α-helix	1075-1102	28
β-strand	1104	1	91
α-helix	1105-1120	16
α-helix	1128-1131	4
α-helix	1137-1145	9
α-helix	1150-1153	4
α-helix	1158-1164	7
α-helix	1168-1170	3
α-helix	1171-1180	10
β-strand	1184-1192	9	92
β-strand	1197-1206	10	92
α-helix	1212-1215	4
β-strand	1218-1226	9	93
β-strand	1232	1	91
β-strand	1233-1242	10	93
β-strand	1250-1257	8	92
β-strand	1265-1272	8	93
β-strand	1279-1285	7	93
α-helix	1291-1300	10
α-helix	1305-1307	3
β-strand	1308	1	94
α-helix	1309-1311	3
α-helix	1315-1322	8
β-strand	1327	1	94
α-helix	1330-1341	12
β-strand	1346-1349	4	95
α-helix	1357-1370	14
β-strand	1376-1379	4	95
α-helix	1383-1393	11
α-helix	1394-1398	5
β-strand	1405-1407	3	95
α-helix	1412-1421	10
β-strand	1424-1427	4	95
α-helix	1429-1437	9
α-helix	1443-1446	4
β-strand	1450-1454	5	95
α-helix	1456-1460	5
α-helix	1464-1480	17
α-helix	1484-1485	2
β-strand	1486-1491	6	95
β-strand	1494	1	96
α-helix	1497-1504	8
β-strand	1511-1513	3	95
α-helix	1516-1518	3
β-strand	1523-1530	8	97
α-helix	1535-1541	7
α-helix	1543-1553	11
β-strand	1559-1563	5	97
α-helix	1566-1582	17
β-strand	1590	1	98
α-helix	1598-1603	6
α-helix	1607-1614	8
β-strand	1617-1620	4	97
α-helix	1626-1638	13
β-strand	1641	1	98
β-strand	1643-1647	5	97
α-helix	1648-1650	3
β-strand	1660-1663	4	97
β-strand	1667-1670	4	99
β-strand	1675-1678	4	99
α-helix	1679-1680	2
α-helix	1681-1689	9
β-strand	1700-1707	8	97
α-helix	1711-1718	8
α-helix	1721	1
β-strand	1722	1	96
α-helix	1723	1
α-helix	1732-1741	10
β-strand	1747	1	100
α-helix	1748-1755	8
α-helix	1759-1766	8
α-helix	1778-1798	21
β-strand	1802-1803	2	101
β-strand	1809	1	100
β-strand	1811-1812	2	101
α-helix	1814-1821	8
α-helix	1826-1835	10
α-helix	1842-1850	9
α-helix	1853-1855	3
α-helix	1864-1874	11
α-helix	1887-1900	14
α-helix	1906-1933	28
β-strand	1935	1	102
α-helix	1937-1951	15
α-helix	1959-1962	4
α-helix	1968-1977	10
α-helix	1982-1986	5
α-helix	1990-1996	7
α-helix	2001-2013	13
β-strand	2017-2023	7	103
β-strand	2030	1	104
β-strand	2034-2043	10	103
α-helix	2046-2047	2
β-strand	2064-2070	7	102
β-strand	2075-2082	8	102
β-strand	2087-2095	9	103
β-strand	2101-2110	10	102
β-strand	2118-2125	8	102
β-strand	2127	1	104

50 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
U2 snRNA	2	RNA	188	Homo sapiens
Splicing factor ESS-2 homolog	4	protein	476	Homo sapiens	Q96DF8 (AlphaFold model)
U5 snRNA	5	RNA	116	Homo sapiens
U6 snRNA	6	RNA	106	Homo sapiens
Eukaryotic initiation factor 4A-III	7	protein	411	Homo sapiens	P38919 (AlphaFold model)
RNA-binding protein 8A	8	protein	174	Homo sapiens	Q9Y5S9 (AlphaFold model)
Protein mago nashi homolog	9	protein	146	Homo sapiens	P61326 (AlphaFold model)
Pre-mRNA-processing-splicing factor 8	A	protein	2335	Homo sapiens	Q6P2Q9
U5 small nuclear ribonucleoprotein 200 kDa helicase	B	protein	2136	Homo sapiens	O75643
116 kDa U5 small nuclear ribonucleoprotein component	C	protein	972	Homo sapiens	Q15029
Peptidyl-prolyl cis-trans isomerase-like 3	C3	protein	161	Homo sapiens	Q9H2H8
Probable ATP-dependent RNA helicase DDX41	CD	protein	622	Homo sapiens	Q9UJV9

41 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>8C6J_1 U2 snRNA (chains 2)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC

Sequence of entity 2 (4), FASTA

>8C6J_2 Splicing factor ESS-2 homolog (chains 4)
METPGASASSLLLPAASRPPRKREAGEAGAATSKQRVLDEEEYIEGLQTVIQRDFFPDVE
KLQAQKEYLEAEENGDLERMRQIAIKFGSALGKMSREPPPPYVTPATFETPEVHAGTGVV
GNKPRPRGRGLEDGEAGEEEEKEPLPSLDVFLSRYTSEDNASFQEIMEVAKERSRARHAW
LYQAEEEFEKRQKDNLELPSAEHQAIESSQASVETWKYKAKNSLMYYPEGVPDEEQLFKK
PRQVVHKNTRFLRDPFSQALSRCQLQQAAALNAQHKQGKVGPDGKELIPQESPRVGGFGF
VATPSPAPGVNESPMMTWGEVENTPLRVEGSETPYVDRTPGPAFKILEPGRRERLGLKMA
NEAAAKNRAKKQEALRRVTENLASLTPKGLSPAMSPALQRLVSRTASKYTDRALRASYTP
SPARSTHLKTPASGLQTPTSTPAPGSATRTPLTQDPASITDNLLQLPARRKASDFF

Sequence of entity 3 (5), FASTA

>8C6J_3 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGCCUUGCCUUGGCAAGGCUA

Sequence of entity 4 (6), FASTA

>8C6J_4 U6 snRNA (chains 6)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUU

Sequence of entity 5 (7), FASTA

>8C6J_5 Eukaryotic initiation factor 4A-III (chains 7)
MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK
PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV
QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA
IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL
VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA
NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL
YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

Sequence of entity 6 (8), FASTA

>8C6J_6 RNA-binding protein 8A (chains 8)
MADVLDLHEAGGEDFAMDEDGDESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD
GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE
YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR

Sequence of entity 7 (9), FASTA

>8C6J_7 Protein mago nashi homolog (chains 9)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 8 (A), FASTA

>8C6J_8 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

Sequence of entity 9 (B), FASTA

>8C6J_9 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains B)
MADVTARSLQYEYKANSNLVLQADRSLIDRTRRDEPTGEVLSLVGKLEGTRMGDKAQRTK
PQMQEERRAKRRKRDEDRHDINKMKGYTLLSEGIDEMVGIIYKPKTKETRETYEVLLSFI
QAALGDQPRDILCGAADEVLAVLKNEKLRDKERRKEIDLLLGQTDDTRYHVLVNLGKKIT
DYGGDKEIQNMDDNIDETYGVNVQFESDEEEGDEDVYGEVREEASDDDMEGDEAVVRCTL
SANLVASGELMSSKKKDLHPRDIDAFWLQRQLSRFYDDAIVSQKKADEVLEILKTASDDR
ECENQLVLLLGFNTFDFIKVLRQHRMMILYCTLLASAQSEAEKERIMGKMEADPELSKFL
YQLHETEKEDLIREERSRRERVRQSRMDTDLETMDLDQGGEALAPRQVLDLEDLVFTQGS
HFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKT
LNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIY
IAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKG
GERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYED
VATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQ
VLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPY
GFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGR
WTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDM
LNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTA
ALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSL
SSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMAD
MVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVV
KKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKV
ELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFE
PLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESL
YQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYIT
PMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWK
QRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDV
AHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVI
VFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYL
HEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYP
IYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEI
VTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSK
CISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPI
RHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAI
RLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVE
SVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQ
LEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATG
AHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD

Sequence of entity 10 (C), FASTA

>8C6J_10 116 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 11 (C3), FASTA

>8C6J_11 Peptidyl-prolyl cis-trans isomerase-like 3 (chains C3)
MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG
RGGNSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGK
VIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPFAQ

Sequence of entity 12 (CD), FASTA

>8C6J_12 Probable ATP-dependent RNA helicase DDX41 (chains CD)
MEESEPERKRARTDEVPAGGSRSEAEDEDDEDYVPYVPLRQRRQLLLQKLLQRRRKGAAE
EEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKILESV
AEGRALMSVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPI
KSFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVI
MFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGG
MSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRT
IFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQEVEYVKEEAK
MVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE
GKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKAC
DESVLMDLKALLLEAKQKVPPVLQVLHCGDESMLDIGGERGCAFCGGLGHRITDCPKLEA
MQTKQVSNIGRKDYLAHSSMDF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	7

Water and common crystallization additives (K) are not listed.

Primary citation

Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins. Dybkov, O., Preussner, M., El Ayoubi, L. et al. Sci Adv (2023) 9:eadf1785. DOI 10.1126/sciadv.adf1785 · PubMed

Other PDB entries of the same protein (UniProt Q96DF8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
9XU3 3.0 Å, Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)
9FMD 3.3 Å, Integrative model of the human post-catalytic spliceosome (P-complex)
8RO2 3.5 Å, Integrative Structure of the human intron lariat Spliceosome (ILS'')

Browse structure collections

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