5XJC: Human spliceosome just prior to exon ligation

Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom. Determined by electron microscopy at 3.6 Å resolution. Released 5 Jul 2017.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Human adenovirus 2
Chains: 50
Atoms: 116,421
Mol. weight: 2962.08 kDa
Ligands: IHP, GTP, MG, ADP
Released: 5 Jul 2017

Explore 5XJC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XJC contains 673 α-helices and 497 β-strands across 46 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.

Chains a and h: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-22	6	20
β-strand	27-35	9	20
β-strand	41-49	9	20
β-strand	55-63	9	20
α-helix	65-67	3
β-strand	68-73	6	20

Chain A: 116 helices, 63 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
α-helix	63-72	10
α-helix	79-81	3
α-helix	82-90	9
α-helix	91-94	4
α-helix	95-103	9
β-strand	115-121	7	1
β-strand	127-129	3	1
β-strand	134-135	2	2
α-helix	137-157	21
α-helix	162-164	3
α-helix	174-177	4
α-helix	178-183	6
α-helix	201-204	4
β-strand	228-229	2	3
α-helix	232-241	10
α-helix	243-245	3
α-helix	260-269	10
α-helix	310-315	6
α-helix	334-336	3
β-strand	382	1	4
β-strand	384	1	4
α-helix	398-403	6
α-helix	409-411	3
β-strand	415-416	2	3
β-strand	419-420	2	2
α-helix	421-423	3
α-helix	428-431	4
α-helix	441-459	19
α-helix	473-477	5
β-strand	482-488	7	1
α-helix	489-510	22
β-strand	516-518	3	5
β-strand	524-526	3	5
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	596-598	3
α-helix	599-616	18
α-helix	631-661	31
α-helix	670-672	3
α-helix	677-696	20
α-helix	703-705	3
α-helix	706-722	17
α-helix	733-763	31
α-helix	769-797	29
α-helix	803-819	17
α-helix	822-824	3
β-strand	825	1	6
α-helix	826-827	2
α-helix	835-848	14
α-helix	858-872	15
α-helix	874-886	13
β-strand	894-900	7	7
β-strand	905-910	6	7
α-helix	913-932	20
β-strand	940	1	8
α-helix	948-960	13
β-strand	973-980	8	8
α-helix	985-987	3
α-helix	990-998	9
β-strand	1001	1	6
α-helix	1003-1013	11
β-strand	1016-1019	4	7
β-strand	1022-1025	4	7
α-helix	1037-1053	17
α-helix	1055-1062	8
α-helix	1077-1081	5
β-strand	1085-1091	7	8
β-strand	1094-1101	8	8
α-helix	1103-1116	14
α-helix	1123-1125	3
α-helix	1140-1141	2
α-helix	1144-1158	15
β-strand	1174-1178	5	8
β-strand	1179	1	9
β-strand	1182	1	9
β-strand	1185-1187	3	10
β-strand	1192-1198	7	10
β-strand	1213-1217	5	10
β-strand	1224-1232	9	10
α-helix	1234-1249	16
α-helix	1256-1274	19
α-helix	1277-1280	4
α-helix	1282-1301	20
α-helix	1308-1310	3
α-helix	1313-1317	5
α-helix	1320-1322	3
β-strand	1335-1337	3	11
α-helix	1340-1346	7
β-strand	1352-1354	3	11
α-helix	1368-1371	4
α-helix	1375-1398	24
α-helix	1409-1411	3
α-helix	1419-1423	5
α-helix	1427-1430	4
α-helix	1436-1441	6
α-helix	1443-1446	4
α-helix	1458-1461	4
α-helix	1468-1477	10
α-helix	1480-1485	6
α-helix	1490-1493	4
α-helix	1498-1500	3
α-helix	1506-1509	4
α-helix	1520-1522	3
α-helix	1524-1537	14
α-helix	1539-1542	4
β-strand	1552-1554	3	12
β-strand	1561-1563	3	12
α-helix	1567-1576	10
α-helix	1581-1598	18
β-strand	1606-1611	6	13
α-helix	1612-1615	4
β-strand	1626	1	14
β-strand	1629-1639	11	13
α-helix	1640-1642	3
β-strand	1643-1644	2	13
α-helix	1652-1654	3
β-strand	1655-1667	13	13
α-helix	1676-1689	14
β-strand	1694	1	14
β-strand	1700-1706	7	13
β-strand	1711-1716	6	13
α-helix	1722-1734	13
α-helix	1738-1750	13
α-helix	1759-1762	4
α-helix	1767-1772	6
β-strand	1777-1781	5	15
β-strand	1787-1792	6	16
β-strand	1798-1803	6	16
β-strand	1805-1811	7	15
β-strand	1816-1822	7	15
α-helix	1824-1827	4
α-helix	1833-1851	19
β-strand	1860-1863	4	15
α-helix	1866-1868	3
α-helix	1869-1875	7
α-helix	1876-1878	3
β-strand	1883-1886	4	15
α-helix	1894-1898	5
α-helix	1900-1907	8
β-strand	1913-1918	6	15
α-helix	1923-1925	3
α-helix	1929-1945	17
α-helix	1948-1954	7
α-helix	1973-1995	23
α-helix	1999-2001	3
α-helix	2004-2012	9
α-helix	2071-2080	10
α-helix	2083-2086	4
β-strand	2090-2092	3	17
β-strand	2103-2107	5	17
α-helix	2108-2117	10
β-strand	2125-2131	7	17
α-helix	2132-2133	2
β-strand	2139-2146	8	17
β-strand	2150	1	18
β-strand	2151-2152	2	19
β-strand	2157-2158	2	19
α-helix	2163-2164	2
α-helix	2167-2169	3
β-strand	2173-2181	9	17
α-helix	2190-2202	13
β-strand	2212-2219	8	17
β-strand	2222-2230	9	17
α-helix	2232-2240	9
α-helix	2253-2255	3
β-strand	2256-2258	3	17
β-strand	2260-2264	5	17
β-strand	2270-2274	5	17
β-strand	2280	1	18
β-strand	2296-2298	3	17
α-helix	2300-2303	4
α-helix	2307-2309	3
α-helix	2311-2314	4
α-helix	2321-2325	5

Chains b and i: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-21	6	20
β-strand	26-33	8	20
β-strand	40-48	9	20
β-strand	64-72	9	20
α-helix	74-76	3
β-strand	77-84	8	20
α-helix	85-87	3

Chains c and j: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	14-19	6	20
β-strand	24-32	9	20
β-strand	38-46	9	20
β-strand	53-60	8	20
α-helix	62-64	3
β-strand	65-69	5	20
α-helix	70-71	2
α-helix	76-79	4

Chain C: 47 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	69-73	5
β-strand	78-80	3	21
α-helix	92	1
α-helix	95-97	3
α-helix	116-125	10
β-strand	129-136	8	22
α-helix	142-153	12
α-helix	174-177	4
β-strand	184-191	8	22
β-strand	197-204	8	22
α-helix	209-211	3
α-helix	212-221	10
β-strand	224-230	7	22
α-helix	237-248	12
β-strand	252-258	7	22
α-helix	260-263	4
α-helix	271-292	22
β-strand	307-311	5	22
α-helix	312-314	3
β-strand	316-318	3	22
α-helix	320-330	11
α-helix	336-340	5
β-strand	347-349	3	23
β-strand	356-358	3	23
α-helix	368-369	2
α-helix	370-374	5
α-helix	375-386	12
α-helix	392-399	8
α-helix	405-408	4
α-helix	412-424	13
α-helix	428-437	10
α-helix	441-452	12
β-strand	453	1	24
α-helix	461-467	7
β-strand	475-482	8	25
β-strand	491-495	5	25
β-strand	500-502	3	26
β-strand	507-511	5	25
α-helix	519-521	3
β-strand	524-525	2	25
β-strand	530-534	5	25
β-strand	537-541	5	25
β-strand	543-545	3	26
β-strand	549-552	4	25
β-strand	563-566	4	25
α-helix	576	1
β-strand	577	1	24
α-helix	578-581	4
β-strand	588-594	7	27
α-helix	597-599	3
α-helix	600-613	14
β-strand	618-622	5	27
β-strand	626-631	6	27
α-helix	634-643	10
α-helix	644-648	5
β-strand	653-655	3	27
α-helix	656-658	3
β-strand	659-660	2	27
β-strand	663-666	4	28
β-strand	675-677	3	29
α-helix	678	1
β-strand	684-691	8	29
α-helix	692-693	2
α-helix	694-702	9
α-helix	711-722	12
α-helix	726-730	5
β-strand	732-734	3	29
β-strand	744-747	4	29
α-helix	750-753	4
α-helix	756-776	21
β-strand	784	1	28
β-strand	787-795	9	29
α-helix	801-822	22
β-strand	825-838	14	28
α-helix	840-842	3
α-helix	843-852	10
β-strand	857-863	7	28
β-strand	866-876	11	28
α-helix	883-890	8
β-strand	896-906	11	28
α-helix	916-919	4
α-helix	923-925	3
α-helix	926-928	3
α-helix	929-937	9
α-helix	938-942	5

Chain d: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	21-26	6
α-helix	30-38	9
β-strand	41-46	6	20
β-strand	51-59	9	20
β-strand	65-76	12	20
β-strand	90-101	12	20
α-helix	103-105	3
β-strand	106-111	6	20

Chain D: 89 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	435-438	4	30
β-strand	442-447	6	30
α-helix	452-456	5
β-strand	463	1	31
β-strand	480	1	31
α-helix	483-494	12
β-strand	499-502	4	32
α-helix	510-523	14
β-strand	537-541	5	32
α-helix	545-559	15
β-strand	568	1	32
α-helix	580-582	3
β-strand	586-588	3	32
α-helix	590-599	10
β-strand	609-614	6	32
α-helix	617-621	5
α-helix	625-642	18
β-strand	647-652	6	32
α-helix	658-664	7
α-helix	669-672	4
β-strand	673-675	3	32
α-helix	678-680	3
β-strand	685-692	8	30
α-helix	697-714	18
β-strand	721-724	4	30
α-helix	730-734	5
α-helix	737-744	8
α-helix	761-766	6
α-helix	774-777	4
β-strand	782-784	3	30
α-helix	792-802	11
β-strand	808-811	4	30
α-helix	813-817	5
β-strand	823	1	33
β-strand	825-829	5	30
β-strand	832-835	4	34
β-strand	840-843	4	34
α-helix	844-845	2
α-helix	846-853	8
β-strand	856	1	33
β-strand	865-872	8	30
α-helix	873-875	3
α-helix	876-883	8
α-helix	893-906	14
β-strand	912	1	35
α-helix	913-920	8
α-helix	924-931	8
α-helix	933-936	4
α-helix	940-945	6
α-helix	950-955	6
α-helix	958-966	9
β-strand	970-972	3	36
β-strand	978	1	35
β-strand	979-981	3	36
α-helix	983-991	9
α-helix	995-1004	10
α-helix	1011-1019	9
α-helix	1022-1024	3
α-helix	1031-1033	3
α-helix	1034-1042	9
α-helix	1055-1067	13
α-helix	1075-1102	28
β-strand	1104	1	37
α-helix	1105-1120	16
α-helix	1128-1131	4
α-helix	1137-1145	9
α-helix	1150-1152	3
α-helix	1158-1162	5
α-helix	1168-1170	3
α-helix	1171-1180	10
β-strand	1184-1194	11	38
β-strand	1197-1206	10	38
β-strand	1218-1226	9	39
β-strand	1232	1	37
β-strand	1233-1242	10	39
α-helix	1249	1
β-strand	1250-1257	8	38
β-strand	1265-1272	8	39
β-strand	1279-1285	7	39
α-helix	1291-1302	12
α-helix	1305-1307	3
β-strand	1308	1	40
α-helix	1315-1322	8
β-strand	1327	1	40
α-helix	1330-1339	10
β-strand	1346-1349	4	41
α-helix	1356-1370	15
β-strand	1376-1379	4	41
α-helix	1383-1393	11
α-helix	1394-1399	6
α-helix	1400-1401	2
β-strand	1405-1407	3	41
α-helix	1412-1418	7
β-strand	1419	1	42
β-strand	1422	1	42
β-strand	1424-1427	4	41
α-helix	1431-1437	7
α-helix	1443-1446	4
β-strand	1450-1454	5	41
α-helix	1456-1460	5
α-helix	1465-1480	16
β-strand	1486-1491	6	41
β-strand	1494	1	43
α-helix	1497-1504	8
α-helix	1508-1510	3
β-strand	1511-1513	3	41
β-strand	1523-1530	8	44
α-helix	1535-1541	7
α-helix	1543-1553	11
β-strand	1559-1563	5	44
α-helix	1568-1582	15
β-strand	1590	1	45
α-helix	1594-1601	8
α-helix	1607-1614	8
β-strand	1619-1620	2	44
α-helix	1626-1638	13
β-strand	1641	1	45
β-strand	1643-1647	5	44
α-helix	1648-1651	4
β-strand	1658	1	46
β-strand	1660-1664	5	44
β-strand	1667-1670	4	47
β-strand	1675-1678	4	47
α-helix	1679-1680	2
α-helix	1681-1689	9
β-strand	1691	1	46
β-strand	1700-1707	8	44
α-helix	1711-1717	7
α-helix	1721	1
β-strand	1722	1	43
α-helix	1723	1
α-helix	1733-1741	9
β-strand	1747	1	48
α-helix	1748-1755	8
α-helix	1759-1764	6
α-helix	1768-1770	3
α-helix	1778-1798	21
β-strand	1802-1805	4	48
β-strand	1809-1812	4	48
α-helix	1814-1822	9
α-helix	1826-1835	10
α-helix	1842-1850	9
α-helix	1853-1855	3
α-helix	1867-1873	7
α-helix	1887-1899	13
α-helix	1906-1933	28
β-strand	1935	1	49
α-helix	1936-1951	16
α-helix	1960-1962	3
α-helix	1968-1977	10
α-helix	2001-2013	13
β-strand	2017-2023	7	50
β-strand	2034-2043	10	50
β-strand	2064-2070	7	49
α-helix	2071-2073	3
β-strand	2075-2082	8	49
β-strand	2087-2095	9	50
β-strand	2102-2110	9	49
β-strand	2118-2124	7	49

Chains e and l: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	20
β-strand	38-50	13	20
β-strand	56-65	10	20
β-strand	70-79	10	20
α-helix	81-83	3
β-strand	84-90	7	20

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-processing-splicing factor 8	A	protein	2335	Homo sapiens	Q6P2Q9 (AlphaFold model)
U5 snRNA	B	RNA	117	Homo sapiens
116 kDa U5 small nuclear ribonucleoprotein component	C	protein	972	Homo sapiens	Q15029 (AlphaFold model)
U5 small nuclear ribonucleoprotein 200 kDa helicase	D	protein	2136	Homo sapiens	O75643 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa protein	E	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
U6 snRNA	F	RNA	107	Homo sapiens
pre-mRNA	G	RNA	275	Human adenovirus 2
Homo sapiens small nuclear RNA (U2) gene	H	RNA	188	Homo sapiens
Pre-mRNA-splicing factor SYF1	I	protein	855	Homo sapiens	Q9HCS7
Crooked neck-like protein 1	J	protein	848	Homo sapiens	Q9BZJ0
Pre-mRNA-splicing factor SPF27	K	protein	225	Homo sapiens	O75934
Cell division cycle 5-like protein	L	protein	802	Homo sapiens	Q99459

28 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5XJC_1 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 2 (B), FASTA

>5XJC_2 U5 snRNA (chains B)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 3 (C), FASTA

>5XJC_3 116 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 4 (D), FASTA

>5XJC_4 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains D)
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 5 (E), FASTA

>5XJC_5 U5 small nuclear ribonucleoprotein 40 kDa protein (chains E)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 6 (F), FASTA

>5XJC_6 U6 snRNA (chains F)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUUU

Sequence of entity 7 (G), FASTA

>5XJC_7 pre-mRNA (chains G)
GGGAAUACACGGAAUUCGAGCUCGCCCACUCUUGGAUCGGAAACCCGUCGGCCUCCGAAC
GXGUAAGAGCCUAGCAUGUAGAACUGGUUACCUGCAGCCCAAGCUUGCGUACACCAUCAG
GGUACGUACUAGUACGUACACCAUCAGGGUACGGCUGCACGUCUAGGGCGCAGUAGUCCA
GGGUUUCCUUGAUGAUGUCAUACUUAUCCUGUCCCUUUUUUUUCCACGGCUCGCGGUUGA
GGACAAACUCUUCGCGGUCUUUCCAGUGGGGAUCC

Sequence of entity 8 (H), FASTA

>5XJC_8 Homo sapiens small nuclear RNA (U2) gene (chains H)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC

Sequence of entity 9 (I), FASTA

>5XJC_9 Pre-mRNA-splicing factor SYF1 (chains I)
MVVMARLSRPERPDLVFEEEDLPYEEEIMRNQFSVKCWLRYIEFKQGAPKPRLNQLYERA
LKLLPCSYKLWYRYLKARRAQVKHRCVTDPAYEDVNNCHERAFVFMHKMPRLWLDYCQFL
MDQGRVTHTRRTFDRALRALPITQHSRIWPLYLRFLRSHPLPETAVRGYRRFLKLSPESA
EEYIEYLKSSDRLDEAAQRLATVVNDERFVSKAGKSNYQLWHELCDLISQNPDKVQSLNV
DAIIRGGLTRFTDQLGKLWCSLADYYIRSGHFEKARDVYEEAIRTVMTVRDFTQVFDSYA
QFEESMIAAKMETASELGREEEDDVDLELRLARFEQLISRRPLLLNSVLLRQNPHHVHEW
HKRVALHQGRPREIINTYTEAVQTVDPFKATGKPHTLWVAFAKFYEDNGQLDDARVILEK
ATKVNFKQVDDLASVWCQCGELELRHENYDEALRLLRKATALPARRAEYFDGSEPVQNRV
YKSLKVWSMLADLEESLGTFQSTKAVYDRILDLRIATPQIVINYAMFLEEHKYFEESFKA
YERGISLFKWPNVSDIWSTYLTKFIARYGGRKLERARDLFEQALDGCPPKYAKTLYLLYA
QLEEEWGLARHAMAVYERATRAVEPAQQYDMFNIYIKRAAEIYGVTHTRGIYQKAIEVLS
DEHAREMCLRFADMECKLGEIDRARAIYSFCSQICDPRTTGAFWQTWKDFEVRHGNEDTI
KEMLRIRRSVQATYNTQVNFMASQMLKVSGSATGTVSDLAPGQSGMDDMKLLEQRAEQLA
AEAERDQPLRAQSKILFVRSDASREELAELAQQVNPEEIQLGEDEDEDEMDLEPNEVRLE
QQSVPAAVFGSLKED

Sequence of entity 10 (J), FASTA

>5XJC_10 Crooked neck-like protein 1 (chains J)
MTATVENLTFQKDTLGNAVDKNTSRLELRSYSLAGRHGSTEPLVLAWSSQFRRLTWGCAL
DALHRSPCVAASQHGVTHLIRSSRTPHSTRCRKEDAQPGHHGNGAASVTAQARGQRSVLQ
VPLPVPRSCLFSESFVVSVSSQSRFLASVPGTGVQRSTAADMAASTAAGKQRIPKVAKVK
NKAPAEVQITAEQLLREAKERELELLPPPPQQKITDEEELNDYKLRKRKTFEDNIRKNRT
VISNWIKYAQWEESLKEIQRARSIYERALDVDYRNITLWLKYAEMEMKNRQVNHARNIWD
RAITTLPRVNQFWYKYTYMEEMLGNVAGARQVFERWMEWQPEEQAWHSYINFELRYKEVD
RARTIYERFVLVHPDVKNWIKYARFEEKHAYFAHARKVYERAVEFFGDEHMDEHLYVAFA
KFEENQKEFERVRVIYKYALDRISKQDAQELFKNYTIFEKKFGDRRGIEDIIVSKRRFQY
EEEVKANPHNYDAWFDYLRLVESDAEAEAVREVYERAIANVPPIQEKRHWKRYIYLWINY
ALYEELEAKDPERTRQVYQASLELIPHKKFTFAKMWILYAQFEIRQKNLSLARRALGTSI
GKCPKNKLFKVYIELELQLREFDRCRKLYEKFLEFGPENCTSWIKFAELETILGDIDRAR
AIYELAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRRLLQRTQHVKVWISFAQFEL
SSGKEGSLTKCRQIYEEANKTMRNCEEKEERLMLLESWRSFEEEFGTASDKERVDKLMPE
KVKKRRKVQTDDGSDAGWEEYFDYIFPEDAANQPNLKLLAMAKLWKKQQQEKEDAEHHPD
EDVDESES

Sequence of entity 11 (K), FASTA

>5XJC_11 Pre-mRNA-splicing factor SPF27 (chains K)
MAGTGLVAGEVVVDALPYFDQGYEAPGVREAAAALVEEETRRYRPTKNYLSYLTAPDYSA
FETDIMRNEFERLAARQPIELLSMKRYELPAPSSGQKNDITAWQECVNNSMAQLEHQAVR
IENLELMSQHGCNAWKVYNENLVHMIEHAQKELQKLRKHIQDLNWQRKNMQLTAGSKLRE
MESNWVSLVSKNYEIERTIVQLENEIYQIKQQHGEANKENIRQDF

Sequence of entity 12 (L), FASTA

>5XJC_12 Cell division cycle 5-like protein (chains L)
MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKK
TEWSREEEEKLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKAAQRDNEEETTDDP
RKLKPGEIDPNPETKPARPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEAR
RLAALQKRRELRAAGIEIQKKRKRKRGVDYNAEIPFEKKPALGFYDTSEENYQALDADFR
KLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAILQTSGVSEFTKKRSKLVLPAP
QISDAELQEVVKVGQASEIARQTAEESGITNSASSTLLSEYNVTNNSVALRTPRTPASQD
RILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
EGLTPRSGTTPKPVINSTPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGL
LGLPAPKNDFEIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKA
VQKDLPRPSEVNETILRPLNVEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNKKG
KTVGFGTNNSEHITYLEHNPYEKFSKEELKKAQDVLVQEMEVVKQGMSHGELSSEAYNQV
WEECYSQVLYLPGQSRYTRANLASKKDRIESLEKRLEINRGHMTTEAKRAAKMEKKMKIL
LGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLECLKEDVQRQQER
EKELQHRYADLLLEKETLKSKF

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	11
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ZN	Zinc ion	Zn	7
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

An Atomic Structure of the Human Spliceosome. Zhang, X., Yan, C., Hang, J. et al. Cell (2017) 169:918-929.e14. DOI 10.1016/j.cell.2017.04.033 · 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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