9XU3: PDB entry 9XU3

Name: PDB 9XU3: Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)
Published: 2026-08-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: splicing

Human minor spliceosome exon-ligation-ready C* complex (prior to step-II). Determined by electron microscopy at 3.0 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 64
Atoms: 123,688
Mol. weight: 3323.39 kDa
Ligands: MG, IHP, GTP, ADP
Released: 12 Aug 2026

Explore 9XU3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XU3 contains 722 α-helices and 617 β-strands across 59 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: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	66-67	2
α-helix	70-76	7
β-strand	85-88	4	10
β-strand	93-98	6	11
β-strand	103-108	6	11
β-strand	112-118	7	11
β-strand	123-130	8	11
β-strand	136-141	6	12
β-strand	147-152	6	12
β-strand	156-161	6	12
β-strand	166-172	7	12
β-strand	177-182	6	13
β-strand	192-197	6	13
β-strand	203-207	5	13
β-strand	217-218	2	13
α-helix	225	1
β-strand	226-232	7	14
β-strand	237-242	6	14
β-strand	247-250	4	14
α-helix	253-255	3
α-helix	275-279	5
β-strand	283-288	6	15
β-strand	294-299	6	15
β-strand	303-308	6	15
β-strand	314-319	6	15
α-helix	322-331	10
α-helix	337-352	16
β-strand	361-363	3	16
β-strand	369-374	6	16
β-strand	377-382	6	16
β-strand	387-392	6	16
β-strand	403-406	4	10
β-strand	437-440	4	10
β-strand	447-451	5	10
α-helix	455-457	3
β-strand	467-468	2	10
α-helix	475-485	11

Chain a: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-21	6	137
β-strand	26-33	8	137
β-strand	40-49	10	137
β-strand	63-72	10	137
α-helix	74-76	3
β-strand	77-84	8	137
α-helix	85-87	3

Chain A: 117 helices, 68 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
α-helix	55-57	3
α-helix	60-62	3
α-helix	64-73	10
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	38
β-strand	127-129	3	38
β-strand	134-135	2	39
α-helix	137-157	21
α-helix	163-165	3
α-helix	174-176	3
α-helix	178-181	4
α-helix	185-191	7
α-helix	201-203	3
β-strand	220-221	2	40
β-strand	226-229	4	40
α-helix	232-241	10
α-helix	252-254	3
α-helix	260-269	10
α-helix	310-315	6
α-helix	327-331	5
α-helix	357-358	2
α-helix	371-373	3
α-helix	398-405	8
α-helix	409-412	4
β-strand	415-416	2	40
β-strand	419-420	2	39
α-helix	421-423	3
α-helix	428-432	5
α-helix	434-436	3
α-helix	441-459	19
α-helix	463-465	3
α-helix	473-477	5
β-strand	482-488	7	38
α-helix	489-510	22
β-strand	516-518	3	41
β-strand	524-526	3	41
α-helix	529-531	3
α-helix	532-537	6
α-helix	542-565	24
α-helix	571-583	13
α-helix	585-588	4
α-helix	591-593	3
α-helix	598-616	19
α-helix	631-661	31
α-helix	667-671	5
α-helix	677-696	20
α-helix	706-722	17
α-helix	733-763	31
α-helix	769-797	29
α-helix	803-820	18
α-helix	824-827	4
β-strand	832	1	42
α-helix	835-847	13
α-helix	858-872	15
α-helix	874-887	14
β-strand	894-900	7	43
β-strand	905-910	6	43
α-helix	913-933	21
β-strand	940-941	2	44
α-helix	948-960	13
β-strand	973-980	8	44
β-strand	982	1	45
α-helix	990-997	8
α-helix	1003-1012	10
β-strand	1016-1019	4	43
β-strand	1022-1025	4	43
α-helix	1037-1053	17
α-helix	1055-1062	8
α-helix	1077-1081	5
β-strand	1085-1091	7	44
β-strand	1094-1101	8	44
α-helix	1103-1116	14
α-helix	1124-1127	4
α-helix	1140-1141	2
α-helix	1144-1159	16
β-strand	1167	1	45
β-strand	1174-1178	5	44
β-strand	1179	1	46
β-strand	1182	1	46
β-strand	1185-1189	5	47
β-strand	1192-1198	7	47
α-helix	1203-1205	3
β-strand	1213-1217	5	47
α-helix	1218	1
β-strand	1224-1232	9	47
α-helix	1234-1249	16
α-helix	1256-1274	19
α-helix	1275-1277	3
α-helix	1282-1302	21
α-helix	1314-1317	4
α-helix	1320-1322	3
α-helix	1327-1329	3
β-strand	1335-1337	3	48
α-helix	1340-1343	4
β-strand	1352-1354	3	48
α-helix	1368-1371	4
α-helix	1375-1399	25
α-helix	1409-1411	3
α-helix	1419-1423	5
α-helix	1430-1432	3
α-helix	1436-1442	7
α-helix	1443-1445	3
α-helix	1469-1477	9
α-helix	1480-1485	6
α-helix	1491-1493	3
β-strand	1502-1503	2	49
α-helix	1508-1512	5
α-helix	1520-1525	6
α-helix	1529-1537	9
α-helix	1539-1542	4
β-strand	1552-1554	3	50
β-strand	1561-1563	3	50
α-helix	1567-1576	10
α-helix	1581-1599	19
α-helix	1601-1604	4
β-strand	1606-1611	6	51
α-helix	1616-1620	5
β-strand	1626	1	52
β-strand	1629-1639	11	51
α-helix	1640-1642	3
β-strand	1643-1644	2	51
β-strand	1655-1667	13	51
α-helix	1676-1689	14
β-strand	1694	1	52
β-strand	1700-1706	7	51
β-strand	1711-1716	6	51
α-helix	1722-1736	15
α-helix	1738-1751	14
β-strand	1753-1754	2	49
β-strand	1758-1759	2	53
α-helix	1760-1761	2
α-helix	1767-1772	6
β-strand	1777-1781	5	54
β-strand	1787-1792	6	55
β-strand	1798-1803	6	55
β-strand	1805-1810	6	54
β-strand	1816-1822	7	54
α-helix	1824-1827	4
α-helix	1833-1851	19
β-strand	1860-1863	4	54
α-helix	1866-1868	3
α-helix	1869-1875	7
β-strand	1883-1886	4	54
α-helix	1892-1898	7
α-helix	1900-1908	9
β-strand	1913-1918	6	54
α-helix	1923-1925	3
α-helix	1929-1945	17
α-helix	1947-1953	7
α-helix	1973-1995	23
α-helix	1999-2001	3
α-helix	2004-2012	9
α-helix	2020-2029	10
α-helix	2061-2066	6
α-helix	2073-2078	6
α-helix	2079-2082	4
α-helix	2083-2088	6
β-strand	2090-2092	3	56
β-strand	2104-2107	4	57
α-helix	2108-2116	9
β-strand	2124-2129	6	56
β-strand	2140-2141	2	57
β-strand	2144-2146	3	56
β-strand	2150	1	58
β-strand	2151-2152	2	59
β-strand	2157-2158	2	59
α-helix	2163-2164	2
α-helix	2167-2170	4
β-strand	2174-2181	8	56
α-helix	2190-2202	13
β-strand	2212-2219	8	56
β-strand	2222-2230	9	56
α-helix	2232-2240	9
α-helix	2253-2255	3
β-strand	2256-2258	3	56
β-strand	2261-2264	4	57
β-strand	2270-2272	3	56
β-strand	2273-2274	2	60
β-strand	2280	1	58
β-strand	2296-2297	2	60
α-helix	2317-2320	4

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	14-19	6	137
β-strand	24-32	9	137
β-strand	38-46	9	137
β-strand	53-60	8	137
α-helix	62-64	3
β-strand	65-69	5	137
α-helix	76-79	4

Chain B: 42 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	69-73	5
β-strand	78-81	4	72
α-helix	95-97	3
β-strand	103	1	73
α-helix	109-111	3
α-helix	116-123	8
β-strand	129-136	8	74
α-helix	143-153	11
β-strand	171	1	73
α-helix	172-177	6
β-strand	184-191	8	74
β-strand	197-204	8	74
α-helix	212-221	10
β-strand	224-230	7	74
α-helix	237-248	12
β-strand	252-258	7	74
α-helix	262-265	4
α-helix	271-292	22
β-strand	307-310	4	74
α-helix	312-314	3
β-strand	317-318	2	74
α-helix	320-330	11
α-helix	336-340	5
β-strand	348-350	3	75
β-strand	355-357	3	75
α-helix	360	1
α-helix	361-363	3
β-strand	367	1	75
α-helix	369-371	3
α-helix	374-385	12
α-helix	392-399	8
α-helix	412-424	13
α-helix	428-437	10
α-helix	439-440	2
α-helix	445-452	8
β-strand	453	1	76
α-helix	462-465	4
β-strand	476-483	8	77
β-strand	490-496	7	77
β-strand	501-502	2	78
β-strand	506-509	4	79
β-strand	523-526	4	79
β-strand	530-533	4	77
β-strand	538-541	4	77
β-strand	543-544	2	78
β-strand	549-553	5	77
β-strand	563	1	77
β-strand	566	1	79
β-strand	577	1	76
α-helix	578-580	3
β-strand	588-594	7	80
α-helix	597-599	3
α-helix	600-613	14
β-strand	618-621	4	80
α-helix	626	1
β-strand	627-631	5	80
α-helix	634-646	13
β-strand	653-655	3	80
α-helix	656-658	3
β-strand	659-660	2	80
β-strand	663-666	4	81
β-strand	674-676	3	82
β-strand	685-691	7	82
α-helix	696-701	6
α-helix	711-722	12
α-helix	726-730	5
β-strand	732-733	2	82
β-strand	743-746	4	82
α-helix	756-760	5
α-helix	763-776	14
β-strand	784	1	81
β-strand	787-794	8	82
α-helix	808-821	14
β-strand	825-838	14	81
α-helix	843-852	10
β-strand	857-862	6	81
α-helix	863	1
β-strand	869-876	8	81
α-helix	877-879	3
α-helix	883-890	8
β-strand	896-906	11	81
α-helix	926-928	3
α-helix	929-941	13
α-helix	949-952	4

Chain c: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	19-26	8
α-helix	30-38	9
β-strand	42-46	5	137
β-strand	51-59	9	137
β-strand	65-76	12	137
β-strand	90-101	12	137
α-helix	103-105	3
β-strand	106-111	6	137
α-helix	112-113	2

Chain C: 97 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	107-124	18
α-helix	129-144	16
α-helix	150-161	12
α-helix	166-179	14
α-helix	267-272	6
α-helix	279-294	16
α-helix	300-310	11
α-helix	315-323	9
α-helix	325-336	12
α-helix	340-352	13
α-helix	354-364	11
α-helix	419-421	3
β-strand	437-439	3	86
β-strand	442-447	6	86
α-helix	449-456	8
α-helix	469-472	4
α-helix	484-494	11
β-strand	499-502	4	87
α-helix	509-523	15
β-strand	537-541	5	87
α-helix	545-558	14
β-strand	566-568	3	87
α-helix	577-581	5
β-strand	585-588	4	87
α-helix	590-599	10
β-strand	609-615	7	87
α-helix	617-621	5
α-helix	625-642	18
β-strand	647-652	6	87
α-helix	658-665	8
β-strand	673-675	3	87
β-strand	685-692	8	86
α-helix	698-714	17
β-strand	721-725	5	86
α-helix	729-743	15
α-helix	746-748	3
α-helix	763-767	5
α-helix	773-776	4
β-strand	782-785	4	86
α-helix	793-802	10
β-strand	808-811	4	86
β-strand	823	1	88
β-strand	825-829	5	86
β-strand	832-834	3	89
β-strand	841-843	3	89
α-helix	844-845	2
α-helix	846-853	8
β-strand	856	1	88
β-strand	865-872	8	86
α-helix	873-883	11
α-helix	887-889	3
α-helix	893-907	15
α-helix	913-920	8
α-helix	924-931	8
α-helix	933-936	4
α-helix	940-945	6
α-helix	950-966	17
β-strand	971-972	2	90
β-strand	979-980	2	90
α-helix	983-991	9
α-helix	995-1003	9
α-helix	1011-1019	9
α-helix	1034-1043	10
α-helix	1055-1068	14
α-helix	1076-1102	27
β-strand	1104	1	91
α-helix	1105-1120	16
α-helix	1128-1131	4
α-helix	1137-1145	9
α-helix	1153-1155	3
α-helix	1158-1164	7
α-helix	1171-1180	10
β-strand	1184-1185	2	92
β-strand	1188	1	93
β-strand	1191-1192	2	94
β-strand	1197-1201	5	94
β-strand	1202	1	93
β-strand	1204	1	95
β-strand	1205-1206	2	92
α-helix	1209-1210	2
α-helix	1212-1215	4
β-strand	1218-1226	9	96
β-strand	1232	1	91
β-strand	1233-1242	10	96
β-strand	1250	1	95
β-strand	1253-1257	5	94
β-strand	1265-1266	2	97
β-strand	1267-1272	6	96
β-strand	1280-1281	2	96
β-strand	1284-1285	2	97
α-helix	1291-1302	12
β-strand	1308	1	98
α-helix	1309-1311	3
α-helix	1318-1320	3
β-strand	1327	1	98
α-helix	1330-1339	10
β-strand	1346-1349	4	99
α-helix	1356-1370	15
β-strand	1376-1379	4	99
α-helix	1383-1397	15
β-strand	1405-1406	2	99
α-helix	1413-1421	9
β-strand	1424-1427	4	99
α-helix	1429-1436	8
α-helix	1439-1441	3
α-helix	1443-1445	3
β-strand	1450-1453	4	99
α-helix	1456-1458	3
α-helix	1464-1481	18
β-strand	1486-1491	6	99
β-strand	1494	1	100
α-helix	1497-1503	7
β-strand	1511-1513	3	99
α-helix	1516-1518	3
β-strand	1523-1528	6	101
α-helix	1535-1543	9
α-helix	1545-1553	9
β-strand	1559-1563	5	101
α-helix	1566-1582	17
β-strand	1590	1	102
α-helix	1598-1601	4
α-helix	1607-1615	9
β-strand	1617-1620	4	101
α-helix	1626-1638	13
β-strand	1641	1	102
β-strand	1643-1647	5	101
α-helix	1648-1650	3
β-strand	1660-1663	4	101
β-strand	1667-1670	4	103
β-strand	1675-1678	4	103
α-helix	1679-1680	2
α-helix	1681-1690	10
β-strand	1700-1705	6	101
α-helix	1708-1719	12
α-helix	1721	1
β-strand	1722	1	100
α-helix	1723	1
α-helix	1728-1730	3
α-helix	1733-1741	9
β-strand	1747	1	104
α-helix	1748-1756	9
α-helix	1759-1766	8
α-helix	1769-1771	3
α-helix	1778-1798	21
β-strand	1802-1805	4	104
β-strand	1809-1812	4	104
α-helix	1814-1822	9
α-helix	1826-1834	9
α-helix	1842-1850	9
α-helix	1853-1855	3
α-helix	1865-1874	10
α-helix	1887-1900	14
α-helix	1906-1932	27
α-helix	1937-1951	15
α-helix	1968-1977	10
α-helix	1985-1987	3
α-helix	1990-1995	6
α-helix	2002-2013	12
β-strand	2017-2023	7	105
β-strand	2034-2043	10	105
β-strand	2064-2070	7	106
β-strand	2075-2082	8	106
β-strand	2088-2095	8	105
α-helix	2096	1
β-strand	2103-2110	8	106
β-strand	2118-2123	6	106

Chain d: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-11	7
β-strand	17-22	6	137
β-strand	27-35	9	137
β-strand	41-49	9	137
β-strand	55-63	9	137
β-strand	68-73	6	137
α-helix	75-79	5
α-helix	81-84	4

51 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
MSE-U12_5 exon	0	RNA	57	Homo sapiens
MSE-U12_intron-3 exon	1	RNA	277	Homo sapiens
U12 snRNA	2	RNA	150	Homo sapiens
Peptidylprolyl isomerase domain and WD repeat-containing protein 1	4	protein	646	Homo sapiens	Q96BP3 (AlphaFold model)
U5 snRNA	5	RNA	117	Homo sapiens
U6atac snRNA	6	RNA	125	Homo sapiens
Pre-mRNA-processing-splicing factor 8	A	protein	2335	Homo sapiens	Q6P2Q9 (AlphaFold model)
116 kDa U5 small nuclear ribonucleoprotein component	B	protein	972	Homo sapiens	Q15029 (AlphaFold model)
U5 small nuclear ribonucleoprotein 200 kDa helicase	C	protein	2136	Homo sapiens	O75643 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa protein	D	protein	357	Homo sapiens	Q96DI7
Cell division cycle 5-like protein	E	protein	802	Homo sapiens	Q99459
Pre-mRNA-splicing factor SYF1	F	protein	855	Homo sapiens	Q9HCS7

42 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9XU3_1 MSE-U12_5 exon (chains 0)
GAAUACACGGAAUUCGAGCUCGCCCACUCUUGGAUCGGAAACCCGUCGGCCUCCAAG

Sequence of entity 2 (1), FASTA

>9XU3_2 MSE-U12_intron-3 exon (chains 1)
AUAUCCUUUUUAAGCAUGUAGAACUGGUUACCUGCAGCCCAAGCUUGCUGCGAUAUCCGU
ACACCAUCAGGGUACGAGCUAGCCCAUGGCGUACACCAUCAGGGUACGACUAGUAGAUCU
CGUACACCAUCAGGGUACGGAAUUCUCUAGACACGUCUAGGGCGCAGUAGUCCAGGGUUU
CCUUGAUGAUGUUUUUCCUUAACUGCAACUUUGCUCACGCUGUUCAGCAUGUUCAUCAUG
AUCACCAUCUUGACCAACUGCAGGAUCCGGAAGAAUU

Sequence of entity 3 (2), FASTA

>9XU3_3 U12 snRNA (chains 2)
AUGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUUCGGGGUGACGCCCGAAUCCUCACUG
CUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGUCGCCCUCAAGGUGACCCGCCUACUUU
GCGGGAUGCCUGGGAGUUGCGAUCUGCCCG

Sequence of entity 4 (4), FASTA

>9XU3_4 Peptidylprolyl isomerase domain and WD repeat-containing protein 1 (chains 4)
MAAESGSDFQQRRRRRRDPEEPEKTELSERELAVAVAVSQENDEENEERWVGPLPVEATL
AKKRKVLEFERVYLDNLPSASMYERSYMHRDVITHVVCTKTDFIITASHDGHVKFWKKIE
EGIEFVKHFRSHLGVIESIAVSSEGALFCSVGDDKAMKVFDVVNFDMINMLKLGYFPGQC
EWIYCPGDAISSVAASEKSTGKIFIYDGRGDNQPLHIFDKLHTSPLTQIRLNPVYKAVVS
SDKSGMIEYWTGPPHEYKFPKNVNWEYKTDTDLYEFAKCKAYPTSVCFSPDGKKIATIGS
DRKVRIFRFVTGKLMRVFDESLSMFTELQQMRQQLPDMEFGRRMAVERELEKVDAVRLIN
IVFDETGHFVLYGTMLGIKVINVETNRCVRILGKQENIRVMQLALFQGIAKKHRAATTIE
MKASENPVLQNIQADPTIVCTSFKKNRFYMFTKREPEDTKSADSDRDVFNEKPSKEEVMA
ATQAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGF
MIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTP
WLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK

Sequence of entity 5 (5), FASTA

>9XU3_5 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 6 (6), FASTA

>9XU3_6 U6atac snRNA (chains 6)
XUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGAGGCCCUCG
GGCCUGACAACACGCAUACGGUUAAGGCAUUGCCACCUACUUCGUGGCAUCUAACCAUCG
UUUUU

Sequence of entity 7 (A), FASTA

>9XU3_7 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 8 (B), FASTA

>9XU3_8 116 kDa U5 small nuclear ribonucleoprotein component (chains B)
MDTDLYDEFGNYIGPELDSDEDDDELGRETKDLDEMDDDDDDDDVGDHDDDHPGMEVVLH
EDKKYYPTAEEVYGPEVETIVQEEDTQPLTEPIIKPVKTKKFTLMEQTLPVTVYEMDFLA
DLMDNSELIRNVTLCGHLHHGKTCFVDCLIEQTHPEIRKRYDQDLCYTDILFTEQERGVG
IKSTPVTVVLPDTKGKSYLFNIMDTPGHVNFSDEVTAGLRISDGVVLFIDAAEGVMLNTE
RLIKHAVQERLAVTVCINKIDRLILELKLPPTDAYYKLRHIVDEVNGLISMYSTDENLIL
SPLLGNVCFSSSQYSICFTLGSFAKIYADTFGDINYQEFAKRLWGDIYFNPKTRKFTKKA
PTSSSQRSFVEFILEPLYKILAQVVGDVDTSLPRTLDELGIHLTKEELKLNIRPLLRLVC
KKFFGEFTGFVDMCVQHIPSPKVGAKPKIEHTYTGGVDSDLGEAMSDCDPDGPLMCHTTK
MYSTDDGVQFHAFGRVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGRLWISVARYHIE
VNRVPAGNWVLIEGVDQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSEL
PKMLDGLRKVNKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVV
TFCETVVETSSLKCFAETPNKKNKITMIAEPLEKGLAEDIENEVVQITWNRKKLGEFFQT
KYDWDLLAARSIWAFGPDATGPNILVDDTLPSEVDKALLGSVKDSIVQGFQWGTREGPLC
DELIRNVKFKILDAVVAQEPLHRGGGQIIPTARRVVYSAFLMATPRLMEPYYFVEVQAPA
DCVSAVYTVLARRRGHVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTHTQGQAFSLSV
FHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDPMLLE
LAKQDVVLNYPM

Sequence of entity 9 (C), FASTA

>9XU3_9 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains C)
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 (D), FASTA

>9XU3_10 U5 small nuclear ribonucleoprotein 40 kDa protein (chains D)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 11 (E), FASTA

>9XU3_11 Cell division cycle 5-like protein (chains E)
MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKK
TEWSREEEEKLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKAAQRDNEEETTDDP
RKLKPGEIDPNPETKPARPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEAR
RLAALQKRRELRAAGIEIQKKRKRKRGVDYNAEIPFEKKPALGFYDTSEENYQALDADFR
KLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAILQTSGVSEFTKKRSKLVLPAP
QISDAELQEVVKVGQASEIARQTAEESGITNSASSTLLSEYNVTNNSVALRTPRTPASQD
RILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
EGLTPRSGTTPKPVINSTPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGL
LGLPAPKNDFEIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKA
VQKDLPRPSEVNETILRPLNVEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNKKG
KTVGFGTNNSEHITYLEHNPYEKFSKEELKKAQDVLVQEMEVVKQGMSHGELSSEAYNQV
WEECYSQVLYLPGQSRYTRANLASKKDRIESLEKRLEINRGHMTTEAKRAAKMEKKMKIL
LGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLECLKEDVQRQQER
EKELQHRYADLLLEKETLKSKF

Sequence of entity 12 (F), FASTA

>9XU3_12 Pre-mRNA-splicing factor SYF1 (chains F)
MVVMARLSRPERPDLVFEEEDLPYEEEIMRNQFSVKCWLRYIEFKQGAPKPRLNQLYERA
LKLLPCSYKLWYRYLKARRAQVKHRCVTDPAYEDVNNCHERAFVFMHKMPRLWLDYCQFL
MDQGRVTHTRRTFDRALRALPITQHSRIWPLYLRFLRSHPLPETAVRGYRRFLKLSPESA
EEYIEYLKSSDRLDEAAQRLATVVNDERFVSKAGKSNYQLWHELCDLISQNPDKVQSLNV
DAIIRGGLTRFTDQLGKLWCSLADYYIRSGHFEKARDVYEEAIRTVMTVRDFTQVFDSYA
QFEESMIAAKMETASELGREEEDDVDLELRLARFEQLISRRPLLLNSVLLRQNPHHVHEW
HKRVALHQGRPREIINTYTEAVQTVDPFKATGKPHTLWVAFAKFYEDNGQLDDARVILEK
ATKVNFKQVDDLASVWCQCGELELRHENYDEALRLLRKATALPARRAEYFDGSEPVQNRV
YKSLKVWSMLADLEESLGTFQSTKAVYDRILDLRIATPQIVINYAMFLEEHKYFEESFKA
YERGISLFKWPNVSDIWSTYLTKFIARYGGRKLERARDLFEQALDGCPPKYAKTLYLLYA
QLEEEWGLARHAMAVYERATRAVEPAQQYDMFNIYIKRAAEIYGVTHTRGIYQKAIEVLS
DEHAREMCLRFADMECKLGEIDRARAIYSFCSQICDPRTTGAFWQTWKDFEVRHGNEDTI
KEMLRIRRSVQATYNTQVNFMASQMLKVSGSATGTVSDLAPGQSGMDDMKLLEQRAEQLA
AEAERDQPLRAQSKILFVRSDASREELAELAQQVNPEEIQLGEDEDEDEMDLEPNEVRLE
QQSVPAAVFGSLKED

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	9
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ZN	Zinc ion	Zn	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

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

Primary citation

Molecular mechanism of the catalysis for U12-type splicing by the human. Bai, R., Guo, H., Sun, R. et al. Vita (2026). DOI 10.15302/vita.2026.06.0042

Other PDB entries of the same protein (UniProt Q96BP3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A2N 1.65 Å, Crystal Structure of the peptidylprolyl isomerase domain of Human PPWD1
9XTT 2.92 Å, Human minor spliceosome branching-completed C complex (after step-I)
9FMD 3.3 Å, Integrative model of the human post-catalytic spliceosome (P-complex)
8I0W 3.4 Å, The cryo-EM structure of human C complex
5YZG 4.1 Å, The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom…
7A5P 5.0 Å, Human C Complex Spliceosome - Medium-resolution PERIPHERY

Browse structure collections

About this viewer

MolViewer shows 9XU3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.