8Y6O: Pre-mRNA-processing-splicing factor 8

Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part. Determined by electron microscopy at 3.38 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 3.38 Å
Organism: Homo sapiens
Chains: 46
Atoms: 101,492
Mol. weight: 2102.09 kDa
Ligands: MG, ZN, GTP, IHP
Released: 20 Mar 2024

Explore 8Y6O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y6O contains 508 α-helices and 480 β-strands across 41 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 a: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	16-21	6	78
β-strand	26-33	8	78
β-strand	40-49	10	78
β-strand	63-72	10	78
β-strand	77-82	6	78

Chain b: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	14-19	6	78
β-strand	24-31	8	78
β-strand	38-46	9	78
β-strand	53-60	8	78
α-helix	62-64	3
β-strand	65-69	5	78
β-strand	70	1	79
α-helix	76-79	4

Chain c: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	20-24	5
α-helix	30-37	8
β-strand	42-46	5	79
β-strand	51-56	6	79
β-strand	66-76	11	79
β-strand	90-100	11	79
β-strand	101	1	78
β-strand	106-111	6	79
α-helix	112-114	3

Chain C: 109 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
α-helix	47-50	4
β-strand	60	1	2
α-helix	64-72	9
α-helix	86-91	6
α-helix	92-94	3
α-helix	95-104	10
α-helix	106-108	3
β-strand	115-121	7	2
β-strand	127-129	3	2
β-strand	134-135	2	3
α-helix	137-157	21
α-helix	163-165	3
α-helix	174-176	3
α-helix	178-182	5
α-helix	186-189	4
α-helix	201-204	4
β-strand	220	1	4
β-strand	228-229	2	4
α-helix	232-241	10
α-helix	243-245	3
α-helix	260-269	10
α-helix	310-315	6
α-helix	329-331	3
α-helix	335-337	3
α-helix	357-359	3
α-helix	371-373	3
α-helix	379-381	3
α-helix	398-405	8
α-helix	407-408	2
β-strand	415-416	2	4
β-strand	419-420	2	3
α-helix	434-436	3
α-helix	441-459	19
α-helix	463-466	4
α-helix	472-478	7
β-strand	482-488	7	2
α-helix	489-509	21
β-strand	516-518	3	5
β-strand	524-526	3	5
α-helix	532-538	7
α-helix	542-566	25
α-helix	571-583	13
α-helix	585-589	5
α-helix	591-593	3
α-helix	598-616	19
α-helix	630-632	3
α-helix	634-655	22
α-helix	681-696	16
α-helix	699-701	3
α-helix	705-721	17
α-helix	733-763	31
α-helix	769-797	29
α-helix	803-820	18
α-helix	824-827	4
α-helix	835-848	14
α-helix	858-872	15
α-helix	874-887	14
β-strand	894-900	7	6
β-strand	905-910	6	6
α-helix	913-932	20
β-strand	940	1	7
α-helix	948-960	13
β-strand	973-978	6	7
α-helix	990-1000	11
α-helix	1003-1012	10
β-strand	1016-1019	4	6
β-strand	1022-1025	4	6
α-helix	1037-1053	17
α-helix	1055-1062	8
α-helix	1077-1080	4
β-strand	1085-1090	6	7
β-strand	1095-1101	7	7
α-helix	1105-1116	12
α-helix	1123-1125	3
α-helix	1144-1160	17
α-helix	1170-1172	3
β-strand	1174-1178	5	7
β-strand	1179	1	8
β-strand	1182	1	8
β-strand	1185-1187	3	9
β-strand	1192-1198	7	9
β-strand	1213-1217	5	9
β-strand	1224-1232	9	9
α-helix	1234-1249	16
α-helix	1256-1271	16
α-helix	1276-1280	5
α-helix	1282-1303	22
α-helix	1314-1317	4
α-helix	1320-1322	3
β-strand	1332	1	10
β-strand	1334	1	11
α-helix	1337-1340	4
β-strand	1341-1345	5	12
β-strand	1350-1354	5	12
β-strand	1364	1	11
α-helix	1368-1371	4
α-helix	1373-1374	2
α-helix	1375-1399	25
β-strand	1404	1	13
α-helix	1407-1409	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
β-strand	1501-1504	4	14
α-helix	1520-1537	18
α-helix	1539-1542	4
β-strand	1553-1554	2	15
α-helix	1555	1
β-strand	1561-1562	2	15
α-helix	1567-1576	10
α-helix	1581-1599	19
β-strand	1608-1611	4	16
α-helix	1612-1613	2
α-helix	1618-1620	3
β-strand	1629-1632	4	16
β-strand	1639	1	17
β-strand	1653	1	17
β-strand	1659-1667	9	16
α-helix	1676-1689	14
β-strand	1700-1706	7	16
β-strand	1711-1714	4	16
α-helix	1722-1736	15
α-helix	1738-1751	14
β-strand	1753-1755	3	14
α-helix	1758-1762	5
β-strand	1763	1	18
α-helix	1768-1772	5
β-strand	1777-1781	5	19
β-strand	1787-1793	7	20
β-strand	1797-1803	7	20
β-strand	1805-1810	6	19
β-strand	1816-1822	7	19
α-helix	1824-1827	4
α-helix	1834-1851	18
β-strand	1860-1863	4	19
α-helix	1869-1875	7
β-strand	1883-1886	4	19
β-strand	1887	1	18
α-helix	1894-1898	5
α-helix	1900-1908	9
β-strand	1914-1918	5	19
α-helix	1929-1945	17
α-helix	1947-1954	8
α-helix	1973-1995	23
α-helix	2004-2012	9
α-helix	2072-2080	9
α-helix	2086-2088	3
β-strand	2090-2092	3	21
β-strand	2103-2107	5	21
α-helix	2108-2116	9
β-strand	2125-2131	7	21
α-helix	2132-2133	2
β-strand	2139-2147	9	21
β-strand	2150	1	22
β-strand	2151-2152	2	23
β-strand	2157-2158	2	23
α-helix	2163-2164	2
β-strand	2173-2181	9	21
α-helix	2190-2202	13
β-strand	2212-2217	6	21
β-strand	2223-2230	8	21
α-helix	2232-2240	9
α-helix	2253-2255	3
β-strand	2256-2258	3	21
β-strand	2260-2264	5	21
β-strand	2270-2272	3	21
β-strand	2273-2274	2	24
β-strand	2280	1	22
α-helix	2282-2287	6
β-strand	2296-2297	2	24
α-helix	2307-2309	3
α-helix	2311-2315	5
α-helix	2317-2319	3

Chain d: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-22	6	78
β-strand	27-35	9	78
β-strand	41-49	9	78
β-strand	55-63	9	78
α-helix	65-67	3
β-strand	68-73	6	78
α-helix	75-79	5

Chain D: 40 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	104	1	25
α-helix	116-123	8
β-strand	129-136	8	26
α-helix	142-153	12
α-helix	172-177	6
β-strand	185-191	7	26
β-strand	197-204	8	26
α-helix	213-219	7
β-strand	224-230	7	26
β-strand	234	1	26
α-helix	237-248	12
β-strand	252-258	7	26
α-helix	261-265	5
α-helix	271-292	22
α-helix	302-304	3
β-strand	307-311	5	26
α-helix	312-314	3
β-strand	316-318	3	26
α-helix	320-330	11
α-helix	336-339	4
α-helix	340-342	3
β-strand	348-350	3	27
β-strand	355-357	3	27
α-helix	365-366	2
β-strand	367	1	27
α-helix	368-369	2
α-helix	370-374	5
α-helix	375-386	12
α-helix	392-399	8
α-helix	407-409	3
α-helix	412-424	13
α-helix	428-437	10
α-helix	445-452	8
β-strand	453	1	28
α-helix	460-464	5
β-strand	475-483	9	25
β-strand	490-498	9	25
β-strand	501-502	2	29
β-strand	506-510	5	25
α-helix	519-521	3
β-strand	522-526	5	25
β-strand	530-533	4	25
β-strand	538-541	4	25
β-strand	543-544	2	29
β-strand	549-552	4	25
β-strand	563-566	4	25
α-helix	576	1
β-strand	577	1	28
α-helix	578-582	5
β-strand	588-594	7	30
α-helix	597-599	3
α-helix	600-613	14
β-strand	618-621	4	30
β-strand	627-631	5	30
α-helix	634-643	10
α-helix	644-648	5
β-strand	653-655	3	30
α-helix	656-658	3
β-strand	659-660	2	30
β-strand	663-666	4	31
β-strand	674-677	4	32
β-strand	684-691	8	32
α-helix	696-701	6
α-helix	711-722	12
α-helix	726-729	4
β-strand	732-735	4	32
β-strand	743-747	5	32
α-helix	756-775	20
β-strand	783-784	2	31
β-strand	787-795	9	32
α-helix	805-807	3
α-helix	809-822	14
β-strand	825-837	13	31
α-helix	843-851	9
β-strand	856-862	7	31
β-strand	869-876	8	31
α-helix	877-879	3
α-helix	883-890	8
β-strand	896-906	11	31
α-helix	929-941	13

Chain e: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	78
β-strand	41-46	6	78
β-strand	47-49	3	79
β-strand	56-58	3	79
β-strand	61-65	5	78
β-strand	70-74	5	78
β-strand	77-79	3	79
α-helix	81-83	3
β-strand	84-89	6	78

Chain E: 107 helices, 71 β-strands

Element	Residues	Length	Sheet
β-strand	41	1	10
α-helix	64-86	23
α-helix	108-124	17
α-helix	129-143	15
α-helix	150-156	7
α-helix	157-161	5
α-helix	166-179	14
β-strand	201-202	2	20
β-strand	219	1	13
β-strand	242	1	34
α-helix	267-272	6
α-helix	279-294	16
α-helix	299-310	12
α-helix	315-323	9
α-helix	325-335	11
α-helix	340-352	13
α-helix	354-364	11
α-helix	411-413	3
β-strand	427-429	3	35
β-strand	436-439	4	36
β-strand	442-447	6	36
α-helix	448-454	7
β-strand	463	1	37
α-helix	464-466	3
α-helix	469-472	4
β-strand	480	1	37
α-helix	483-486	4
α-helix	489	1
α-helix	490-494	5
β-strand	499-503	5	38
α-helix	509-523	15
α-helix	533-535	3
β-strand	537-541	5	38
α-helix	545-558	14
β-strand	566-568	3	38
α-helix	573-582	10
β-strand	585-588	4	38
α-helix	590-599	10
α-helix	601-605	5
β-strand	609-614	6	38
α-helix	625-642	18
β-strand	647-653	7	38
α-helix	658-664	7
β-strand	673-675	3	38
α-helix	678-680	3
β-strand	685-692	8	36
α-helix	697-714	18
β-strand	721-724	4	36
α-helix	728-744	17
α-helix	748-751	4
α-helix	758-768	11
α-helix	772-777	6
β-strand	784-785	2	36
α-helix	791-802	12
β-strand	808-811	4	36
α-helix	813-818	6
β-strand	823	1	39
β-strand	825-828	4	36
β-strand	832-835	4	40
β-strand	840-843	4	40
α-helix	844-845	2
α-helix	846-854	9
β-strand	856	1	39
β-strand	865-872	8	36
α-helix	875-883	9
α-helix	897-907	11
β-strand	912	1	41
α-helix	913-921	9
α-helix	924-931	8
α-helix	933-936	4
α-helix	940-945	6
α-helix	950-966	17
β-strand	970-972	3	42
β-strand	978	1	41
β-strand	979-981	3	42
α-helix	983-991	9
α-helix	995-1004	10
α-helix	1011-1019	9
α-helix	1022-1024	3
α-helix	1034-1041	8
α-helix	1055-1068	14
α-helix	1075-1102	28
β-strand	1104	1	43
α-helix	1105-1120	16
α-helix	1128-1131	4
α-helix	1137-1145	9
α-helix	1152-1155	4
α-helix	1158-1165	8
α-helix	1168-1170	3
α-helix	1171-1180	10
β-strand	1184-1190	7	44
β-strand	1194	1	45
β-strand	1197	1	45
β-strand	1200-1206	7	44
β-strand	1218-1226	9	46
β-strand	1232	1	43
β-strand	1233-1242	10	46
β-strand	1250-1254	5	44
α-helix	1259	1
α-helix	1262-1263	2
β-strand	1265-1272	8	46
β-strand	1279-1285	7	46
α-helix	1291-1299	9
α-helix	1304-1307	4
β-strand	1308	1	47
α-helix	1309-1311	3
α-helix	1315-1319	5
β-strand	1327	1	47
α-helix	1330-1341	12
β-strand	1346-1349	4	48
α-helix	1357-1370	14
β-strand	1376-1379	4	48
α-helix	1383-1393	11
α-helix	1394-1400	7
β-strand	1405-1407	3	48
α-helix	1412-1420	9
β-strand	1424-1427	4	48
α-helix	1429-1436	8
β-strand	1450-1453	4	48
α-helix	1456-1459	4
α-helix	1464-1481	18
β-strand	1486-1491	6	48
β-strand	1494	1	49
α-helix	1497-1504	8
α-helix	1508-1510	3
β-strand	1511-1513	3	48
α-helix	1516-1518	3
β-strand	1523-1529	7	50
α-helix	1535-1541	7
α-helix	1543-1553	11
β-strand	1559-1563	5	50
α-helix	1566-1582	17
β-strand	1590	1	51
α-helix	1594-1601	8
α-helix	1607-1614	8
β-strand	1617-1620	4	50
α-helix	1626-1638	13
β-strand	1641	1	51
β-strand	1643-1647	5	50
α-helix	1649-1651	3
β-strand	1660-1664	5	50
β-strand	1667-1670	4	52
β-strand	1675-1678	4	52
α-helix	1679-1680	2
α-helix	1681-1689	9
β-strand	1700-1706	7	50
α-helix	1708-1710	3
α-helix	1711-1719	9
α-helix	1721	1
β-strand	1722	1	49
α-helix	1723	1
α-helix	1728-1730	3
α-helix	1732-1741	10
α-helix	1748-1756	9
α-helix	1759-1764	6
α-helix	1768-1771	4
α-helix	1778-1799	22
β-strand	1802-1804	3	53
β-strand	1810-1812	3	53
α-helix	1814-1822	9
α-helix	1826-1835	10
α-helix	1842-1850	9
α-helix	1853-1855	3
α-helix	1867-1874	8
α-helix	1887-1900	14
α-helix	1906-1933	28
α-helix	1936-1951	16
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	54
β-strand	2034-2043	10	54
β-strand	2064-2070	7	55
β-strand	2076-2082	7	55
β-strand	2089-2095	7	54
β-strand	2102-2110	9	55
β-strand	2120-2124	5	55

33 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
pre-mRNA	A	RNA	280	Homo sapiens
U5 snRNA	B	RNA	117	Homo sapiens
Pre-mRNA-processing-splicing factor 8	C	protein	2335	Homo sapiens	Q6P2Q9 (AlphaFold model)
116 kDa U5 small nuclear ribonucleoprotein component	D	protein	972	Homo sapiens	Q15029 (AlphaFold model)
U5 small nuclear ribonucleoprotein 200 kDa helicase	E	protein	2136	Homo sapiens	O75643 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa protein	F	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
Pre-mRNA-processing factor 6	G	protein	941	Homo sapiens	O94906
Thioredoxin-like protein 4B	H	protein	149	Homo sapiens	Q9NX01
Probable ATP-dependent RNA helicase DDX23	I	protein	820	Homo sapiens	Q9BUQ8
Small nuclear ribonucleoprotein-associated proteins B and B'	a, h, o	protein	240	Homo sapiens	P14678
Small nuclear ribonucleoprotein Sm D1	b, i, p	protein	119	Homo sapiens	P62314
Small nuclear ribonucleoprotein Sm D2	c, j, q	protein	118	Homo sapiens	P62316

20 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8Y6O_1 pre-mRNA (chains A)
GAAUACACGGAAUUCGAGCUCGCCCACUCUUGGAUCGGAAACCCGUCGGCCUCCGAAAUA
UCCUUUUCUAGCAUGUAGAACUGGUUACCUGCAGCCCAAGCUUGCUGCGAUAUCCGUACA
CCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGGGUACGACUAGUAGAUCUCGU
ACACCAUCAGGGUACGGAAUUCUCUAGACACGUCUAGGGCGCAGUAGUCCAGGGUUUCCU
UGAUGAUGUCAUAUCCUUAACUCAUUGUCCCUUUUUUUUC

Sequence of entity 2 (B), FASTA

>8Y6O_2 U5 snRNA (chains B)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 3 (C), FASTA

>8Y6O_3 Pre-mRNA-processing-splicing factor 8 (chains C)
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 4 (D), FASTA

>8Y6O_4 116 kDa U5 small nuclear ribonucleoprotein component (chains D)
MDTDLYDEFGNYIGPELDSDEDDDELGRETKDLDEMDDDDDDDDVGDHDDDHPGMEVVLH
EDKKYYPTAEEVYGPEVETIVQEEDTQPLTEPIIKPVKTKKFTLMEQTLPVTVYEMDFLA
DLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHPEIRKRYDQDLCYTDILFTEQERGVG
IKSTPVTVVLPDTKGKSYLFNIMDTPGHVNFSDEVTAGLRISDGVVLFIDAAEGVMLNTE
RLIKHAVQERLAVTVCINKIDRLILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLIL
SPLLGNVCFSSSQYSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRKFTKKA
PTSSSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTKEELKLNIRPLLRLVC
KKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK
MYSTDDGVQFHAFGRVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGRLWISVARYHIE
VNRVPAGNWVLIEGVDQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSEL
PKMLDGLRKVNKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVV
TFCETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVVQITWNRKKLGEFFQT
KYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVDKALLGSVKDSIVQGFQWGTREGPLC
DELIRNVKFKILDAVVAQEPLHRGGGQIIPTARRVVYSAFLMATPRLMEPYYFVEVQAPA
DCVSAVYTVLARRRGHVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSV
FHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDPMLLE
LAKQDVVLNYPM

Sequence of entity 5 (E), FASTA

>8Y6O_5 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains E)
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 6 (F), FASTA

>8Y6O_6 U5 small nuclear ribonucleoprotein 40 kDa protein (chains F)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 7 (G), FASTA

>8Y6O_7 Pre-mRNA-processing factor 6 (chains G)
MNKKKKPFLGMPAPLGYVPGLGRGATGFTTRSDIGPARDANDPVDDRHAPPGKRTVGDQM
KKNQAADDDDEDLNDTNYDEFNGYAGSLFSSGPYEKDDEEADAIYAALDKRMDERRKERR
EQREKEEIEKYRMERPKIQQQFSDLKRKLAEVTEEEWLSIPEVGDARNKRQRNPRYEKLT
PVPDSFFAKHLQTGENHTSVDPRQTQFGGLNTPYPGGLNTPYPGGMTPGLMTPGTGELDM
RKIGQARNTLMDMRLSQVSDSVSGQTVVDPKGYLTDLNSMIPTHGGDINDIKKARLLLKS
VRETNPHHPPAWIASARLEEVTGKLQVARNLIMKGTEMCPKSEDVWLEAARLQPGDTAKA
VVAQAVRHLPQSVRIYIRAAELETDIRAKKRVLRKALEHVPNSVRLWKAAVELEEPEDAR
IMLSRAVECCPTSVELWLALARLETYENARKVLNKARENIPTDRHIWITAAKLEEANGNT
QMVEKIIDRAITSLRANGVEINREQWIQDAEECDRAGSVATCQAVMRAVIGIGIEEEDRK
HTWMEDADSCVAHNALECARAIYAYALQVFPSKKSVWLRAAYFEKNHGTRESLEALLQRA
VAHCPKAEVLWLMGAKSKWLAGDVPAARSILALAFQANPNSEEIWLAAVKLESENDEYER
ARRLLAKARSSAPTARVFMKSVKLEWVQDNIRAAQDLCEEALRHYEDFPKLWMMKGQIEE
QKEMMEKAREAYNQGLKKCPHSTPLWLLLSRLEEKIGQLTRARAILEKSRLKNPKNPGLW
LESVRLEYRAGLKNIANTLMAKALQECPNSGILWSEAIFLEARPQRRTKSVDALKKCEHD
PHVLLAVAKLFWSQRKITKAREWFHRTVKIDSDLGDAWAFFYKFELQHGTEEQQEEVRKR
CESAEPRHGELWCAVSKDIANWQKKIGDILRLVAGRIKNTF

Sequence of entity 8 (H), FASTA

>8Y6O_8 Thioredoxin-like protein 4B (chains H)
MSFLLPKLTSKKEVDQAIKSTAEKVLVLRFGRDEDPVCLQLDDILSKTSSDLSKMAAIYL
VDVDQTAVYTQYFDISYIPSTVFFFNGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIY
RGAMRGKLIVQSPIDPKNIPKYDLLYQDI

Sequence of entity 9 (I), FASTA

>8Y6O_9 Probable ATP-dependent RNA helicase DDX23 (chains I)
MAGELADKKDRDASPSKEERKRSRTPDRERDRDRDRKSSPSKDRKRHRSRDRRRGGSRSR
SRSRSKSAERERRHKERERDKERDRNKKDRDRDKDGHRRDKDRKRSSLSPGRGKDFKSRK
DRDSKKDEEDEHGDKKPKAQPLSLEELLAKKKAEEEAEAKPKFLSKAEREAEALKRRQQE
VEERQRMLEEERKKRKQFQDLGRKMLEDPQERERRERRERMERETNGNEDEEGRQKIREE
KDKSKELHAIKERYLGGIKKRRRTRHLNDRKFVFEWDASEDTSIDYNPLYKERHQVQLLG
RGFIAGIDLKQQKREQSRFYGDLMEKRRTLEEKEQEEARLRKLRKKEAKQRWDDRHWSQK
KLDEMTDRDWRIFREDYSITTKGGKIPNPIRSWKDSSLPPHILEVIDKCGYKEPTPIQRQ
AIPIGLQNRDIIGVAETGSGKTAAFLIPLLVWITTLPKIDRIEESDQGPYAIILAPTREL
AQQIEEETIKFGKPLGIRTVAVIGGISREDQGFRLRMGCEIVIATPGRLIDVLENRYLVL
SRCTYVVLDEADRMIDMGFEPDVQKILEHMPVSNQKPDTDEAEDPEKMLANFESGKHKYR
QTVMFTATMPPAVERLARSYLRRPAVVYIGSAGKPHERVEQKVFLMSESEKRKKLLAILE
QGFDPPIIIFVNQKKGCDVLAKSLEKMGYNACTLHGGKGQEQREFALSNLKAGAKDILVA
TDVAGRGIDIQDVSMVVNYDMAKNIEDYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELK
QAILESPVSSCPPELANHPDAQHKPGTILTKKRREETIFA

Sequence of entity 10 (a, h, o), FASTA

>8Y6O_10 Small nuclear ribonucleoprotein-associated proteins B and B' (chains a, h, o)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP

Sequence of entity 11 (b, i, p), FASTA

>8Y6O_11 Small nuclear ribonucleoprotein Sm D1 (chains b, i, p)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Sequence of entity 12 (c, j, q), FASTA

>8Y6O_12 Small nuclear ribonucleoprotein Sm D2 (chains c, j, q)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	6
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Bai, R., Yuan, M., Zhang, P. et al. Science (2024) 383:1245-1252. DOI 10.1126/science.adn7272 · PubMed

Other PDB entries of the same protein (UniProt Q6P2Q9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JK8 1.15 Å, Open and closed forms of R1865A human PRP8 RNase H-like domain with bound Mg ion
4JKB 1.3 Å, Open and closed forms of V1788D human PRP8 RNase H-like domain with bound Mg ion
4JKA 1.32 Å, Open and closed forms of R1865A human PRP8 RNase H-like domain with bound Co ion
4JK7 1.4 Å, Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Mg ion
4JK9 1.5 Å, Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Co ion
4JKC 1.5 Å, Open and closed forms of T1800E human PRP8 RNase H-like domain with bound Mg ion
4JKD 1.55 Å, Open and closed forms of I1790Y human PRP8 RNase H-like domain with bound Mg ion
4JKE 1.65 Å, Open and closed forms of T1789P human PRP8 RNase H-like domain with bound Mg ion
4JKG 1.8 Å, Open and closed forms of mixed T1789P+R1865A and R1865A human PRP8 RNase H-like domain…
4JKH 1.8 Å, Open and closed forms of D1781E human PRP8 RNase H-like domain with bound Mg ion
3ENB 1.85 Å, Crystal Structure of PRP8 core domain IV
3LRU 1.85 Å, hPRP8 Non-Native Subdomain

Browse structure collections

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