5O9Z: Pre-mRNA-processing-splicing factor 8

Name: PDB 5O9Z: Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex)
Published: 2017-08-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: splicing

Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex). Determined by electron microscopy at 4.5 Å resolution. Released 16 Aug 2017.

Method: Electron microscopy
Resolution: 4.5 Å
Organism: Homo sapiens
Chains: 57
Atoms: 59,243
Mol. weight: 2389.15 kDa
Released: 16 Aug 2017

Explore 5O9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O9Z contains 370 α-helices and 331 β-strands across 31 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	27-37	11
β-strand	42-46	5	76
β-strand	51-59	9	76
β-strand	65-73	9	76
β-strand	93-101	9	76
β-strand	106-110	5	76

Chain A: 97 helices, 55 β-strands

Element	Residues	Length	Sheet
α-helix	64-72	9
α-helix	81-92	12
α-helix	97-103	7
β-strand	116-121	6	1
β-strand	127-128	2	1
α-helix	137-156	20
α-helix	177-181	5
α-helix	194-196	3
α-helix	204-208	5
α-helix	210-215	6
β-strand	228-229	2	2
α-helix	232-242	11
α-helix	252-257	6
α-helix	260-268	9
α-helix	310-315	6
α-helix	332-334	3
α-helix	357-358	2
α-helix	371-379	9
α-helix	398-404	7
α-helix	409-412	4
β-strand	415-416	2	2
α-helix	428-432	5
α-helix	442-459	18
α-helix	472-477	6
β-strand	482-487	6	1
α-helix	489-510	22
α-helix	532-536	5
α-helix	543-567	25
α-helix	572-587	16
α-helix	597-616	20
α-helix	632-659	28
α-helix	679-696	18
α-helix	706-721	16
α-helix	733-763	31
α-helix	770-796	27
α-helix	803-820	18
β-strand	825	1	3
α-helix	826-829	4
α-helix	835-850	16
α-helix	858-872	15
α-helix	874-887	14
β-strand	894-899	6	4
β-strand	906-910	5	4
α-helix	913-932	20
α-helix	949-960	12
β-strand	973-980	8	5
α-helix	990-1000	11
β-strand	1001	1	3
α-helix	1003-1014	12
β-strand	1016-1019	4	4
β-strand	1022-1025	4	4
α-helix	1037-1062	26
α-helix	1077-1082	6
β-strand	1085-1091	7	5
β-strand	1094-1101	8	5
α-helix	1103-1116	14
α-helix	1140-1141	2
α-helix	1144-1160	17
α-helix	1162	1
β-strand	1174-1178	5	5
β-strand	1185-1187	3	6
β-strand	1193-1198	6	6
α-helix	1199-1201	3
β-strand	1214-1217	4	6
β-strand	1224-1231	8	6
α-helix	1234-1247	14
α-helix	1256-1270	15
α-helix	1275-1280	6
α-helix	1282-1303	22
α-helix	1313-1317	5
α-helix	1320-1322	3
α-helix	1334-1336	3
α-helix	1337-1339	3
β-strand	1341-1345	5	7
β-strand	1350-1354	5	7
α-helix	1365-1367	3
α-helix	1373-1374	2
α-helix	1375-1398	24
α-helix	1405-1408	4
α-helix	1419-1423	5
α-helix	1425-1429	5
α-helix	1436-1446	11
α-helix	1468-1477	10
α-helix	1480-1487	8
α-helix	1490-1493	4
α-helix	1508-1516	9
α-helix	1520-1526	7
α-helix	1529-1537	9
α-helix	1539-1542	4
α-helix	1567-1577	11
α-helix	1581-1599	19
β-strand	1606-1611	6	8
α-helix	1616-1620	5
β-strand	1629-1633	5	8
β-strand	1639	1	9
α-helix	1640-1641	2
β-strand	1643-1644	2	10
β-strand	1655	1	9
β-strand	1659-1660	2	8
β-strand	1662-1667	6	10
α-helix	1677-1689	13
β-strand	1701-1706	6	10
β-strand	1711-1716	6	10
α-helix	1722-1735	14
α-helix	1738-1750	13
β-strand	1779-1781	3	11
β-strand	1788-1790	3	12
β-strand	1800-1802	3	12
β-strand	1805-1810	6	11
β-strand	1816-1822	7	11
α-helix	1833-1839	7
α-helix	1841-1850	10
α-helix	1854-1856	3
β-strand	1862-1863	2	11
α-helix	1870-1875	6
α-helix	1883-1884	2
β-strand	1885	1	11
α-helix	1890-1891	2
α-helix	1893-1897	5
α-helix	1900-1907	8
β-strand	1914-1918	5	11
α-helix	1921-1925	5
α-helix	1929-1945	17
α-helix	1947-1953	7
β-strand	1961	1	13
α-helix	1969	1
β-strand	1970	1	13
α-helix	1973-1995	23
α-helix	2004-2012	9
α-helix	2070-2088	19
β-strand	2090-2092	3	14
β-strand	2103-2106	4	14
α-helix	2108-2117	10
β-strand	2125-2131	7	14
β-strand	2139-2146	8	14
β-strand	2150	1	15
β-strand	2151-2152	2	16
β-strand	2157-2158	2	16
α-helix	2162-2164	3
β-strand	2173-2180	8	14
α-helix	2188-2189	2
α-helix	2190-2202	13
β-strand	2212-2219	8	14
β-strand	2222-2230	9	14
α-helix	2232-2240	9
α-helix	2253-2255	3
β-strand	2256-2258	3	14
β-strand	2260-2263	4	14
β-strand	2270-2274	5	14
β-strand	2280	1	15
β-strand	2296-2298	3	14
α-helix	2307-2309	3

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
β-strand	17-23	7	76
β-strand	28-35	8	76
β-strand	43-51	9	76
β-strand	54-58	5	76
β-strand	61-64	4	76
α-helix	66-68	3
β-strand	69-73	5	76

Chain B: 40 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	116-123	8
β-strand	130-136	7	18
α-helix	142-153	12
α-helix	172-177	6
β-strand	185-190	6	18
β-strand	198-204	7	18
α-helix	209-219	11
β-strand	224-230	7	18
β-strand	234	1	18
α-helix	237-248	12
β-strand	252-258	7	18
α-helix	260-263	4
α-helix	271-292	22
α-helix	302-306	5
β-strand	307-309	3	18
β-strand	310-311	2	19
β-strand	316-317	2	19
α-helix	320-331	12
α-helix	336-339	4
α-helix	340-343	4
β-strand	348-350	3	20
β-strand	355-357	3	20
α-helix	360-361	2
β-strand	367	1	20
α-helix	368	1
α-helix	369-374	6
α-helix	375-385	11
α-helix	388-397	10
α-helix	405-408	4
α-helix	412-423	12
α-helix	428-432	5
α-helix	439-440	2
α-helix	441-452	12
β-strand	453	1	21
α-helix	460-464	5
β-strand	475-483	9	22
β-strand	490-498	9	22
β-strand	501-502	2	23
β-strand	506-510	5	22
β-strand	522-526	5	22
β-strand	530-534	5	22
β-strand	537-540	4	22
β-strand	543-544	2	23
β-strand	549-552	4	22
β-strand	563-566	4	22
β-strand	577	1	21
β-strand	589-594	6	24
α-helix	597-599	3
α-helix	600-613	14
β-strand	619-621	3	24
β-strand	627-630	4	24
α-helix	634-643	10
α-helix	644-648	5
β-strand	653-655	3	24
α-helix	656-658	3
β-strand	659	1	24
β-strand	663-666	4	25
β-strand	674-677	4	26
β-strand	684-691	8	26
α-helix	694-701	8
α-helix	711-721	11
α-helix	726-729	4
β-strand	732	1	26
α-helix	737-739	3
β-strand	743-747	5	26
α-helix	751-754	4
α-helix	756-761	6
α-helix	763-774	12
β-strand	784	1	25
β-strand	787-794	8	26
α-helix	805-807	3
α-helix	809-822	14
β-strand	825-829	5	25
β-strand	831-838	8	27
α-helix	840-852	13
β-strand	856-861	6	27
β-strand	869-876	8	27
α-helix	883-890	8
β-strand	900-901	2	27
β-strand	905-906	2	25
α-helix	928-941	14
α-helix	949-952	4

Chain c: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
β-strand	32-36	5	76
β-strand	42-50	9	76
β-strand	56-64	9	76
β-strand	73-79	7	76
β-strand	86-89	4	76

Chain C: 83 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	435-438	4	28
β-strand	442-446	5	28
α-helix	449-455	7
α-helix	461	1
β-strand	462-463	2	29
α-helix	464-466	3
β-strand	480-481	2	29
α-helix	483-494	12
β-strand	499-502	4	30
α-helix	509-523	15
β-strand	538-541	4	30
α-helix	545-562	18
α-helix	577-581	5
β-strand	586-588	3	30
α-helix	590-596	7
α-helix	597-601	5
β-strand	611-614	4	30
α-helix	617-620	4
α-helix	625-642	18
β-strand	647-652	6	30
α-helix	658-664	7
α-helix	669-672	4
β-strand	673-675	3	30
α-helix	678-680	3
β-strand	685-686	2	28
β-strand	688-692	5	28
α-helix	697-714	18
β-strand	721-724	4	28
α-helix	729-743	15
α-helix	761-766	6
α-helix	778-780	3
α-helix	791-802	12
β-strand	808	1	28
β-strand	811	1	28
α-helix	813-817	5
β-strand	823	1	31
β-strand	825-828	4	28
β-strand	834	1	32
β-strand	841	1	32
α-helix	846-854	9
β-strand	856-857	2	31
β-strand	865-872	8	28
α-helix	873-880	8
α-helix	887-889	3
α-helix	893-906	14
β-strand	912	1	33
α-helix	913-921	9
α-helix	924-931	8
α-helix	940-945	6
α-helix	950-955	6
α-helix	958-966	9
β-strand	970-972	3	34
β-strand	978	1	33
β-strand	979-981	3	34
α-helix	983-990	8
α-helix	995-1003	9
α-helix	1011-1019	9
α-helix	1031-1039	9
α-helix	1055-1067	13
α-helix	1078-1102	25
β-strand	1104	1	35
α-helix	1105-1120	16
α-helix	1128-1132	5
α-helix	1137-1146	10
α-helix	1151-1154	4
α-helix	1158-1161	4
α-helix	1168-1179	12
β-strand	1184-1192	9	36
β-strand	1198-1206	9	36
α-helix	1212-1215	4
β-strand	1218-1226	9	37
β-strand	1232	1	35
β-strand	1233-1242	10	37
β-strand	1250-1253	4	36
β-strand	1265-1266	2	38
β-strand	1267-1272	6	37
β-strand	1279-1281	3	37
β-strand	1284-1285	2	38
α-helix	1301-1303	3
β-strand	1307-1308	2	39
α-helix	1309-1311	3
α-helix	1315-1322	8
β-strand	1327-1328	2	39
α-helix	1330-1340	11
β-strand	1347-1349	3	40
α-helix	1356-1370	15
β-strand	1376-1379	4	40
α-helix	1383-1394	12
α-helix	1395-1400	6
β-strand	1405-1407	3	40
α-helix	1412-1418	7
β-strand	1424-1427	4	40
α-helix	1429-1437	9
α-helix	1443-1446	4
β-strand	1450-1454	5	40
α-helix	1456-1459	4
α-helix	1464-1480	17
β-strand	1486-1491	6	40
α-helix	1497-1503	7
β-strand	1512	1	40
β-strand	1523-1528	6	41
α-helix	1535-1540	6
α-helix	1543-1550	8
β-strand	1559-1563	5	42
α-helix	1567-1582	16
β-strand	1590	1	43
α-helix	1598-1602	5
α-helix	1607-1614	8
α-helix	1626-1637	12
β-strand	1641	1	43
β-strand	1643-1647	5	42
α-helix	1648-1650	3
β-strand	1660-1662	3	42
β-strand	1667-1670	4	44
β-strand	1675-1678	4	44
α-helix	1679-1680	2
α-helix	1681-1689	9
β-strand	1700-1705	6	41
α-helix	1711-1718	8
α-helix	1721-1723	3
α-helix	1733-1741	9
β-strand	1747	1	45
α-helix	1748-1756	9
α-helix	1759-1766	8
α-helix	1768-1771	4
α-helix	1778-1798	21
β-strand	1802-1805	4	45
β-strand	1809-1812	4	45
α-helix	1814-1822	9
α-helix	1826-1833	8
α-helix	1842-1849	8
α-helix	1855-1857	3
α-helix	1864-1873	10
α-helix	1887-1899	13
α-helix	1906-1933	28
β-strand	1935	1	46
α-helix	1936-1951	16
α-helix	1968-1976	9
α-helix	1982-1985	4
α-helix	2001-2012	12
β-strand	2018-2024	7	47
β-strand	2034-2042	9	47
α-helix	2046-2047	2
β-strand	2063-2070	8	46
β-strand	2075-2083	9	46
β-strand	2087-2095	9	47
β-strand	2103-2109	7	46
β-strand	2118-2123	6	46

Chain d: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	16-21	6	76
β-strand	26-31	6	76
β-strand	41-47	7	76
β-strand	55-62	8	76
β-strand	67-71	5	76

Chain e: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-22	6	76
β-strand	27-35	9	76
β-strand	41-49	9	76
β-strand	55-63	9	76
β-strand	68-72	5	76

23 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)
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 (AlphaFold model)
U4/U6 small nuclear ribonucleoprotein Prp3	E	protein	683	Homo sapiens	O43395
U4/U6 small nuclear ribonucleoprotein Prp4	F	protein	521	Homo sapiens	O43172
Pre-mRNA-processing factor 6	G	protein	941	Homo sapiens	O94906
U4/U6 small nuclear ribonucleoprotein Prp31	H	protein	499	Homo sapiens	Q8WWY3
Pre-mRNA-splicing factor 38A	I	protein	312	Homo sapiens	Q8NAV1
Thioredoxin-like protein 4A	J	protein	142	Homo sapiens	P83876
Microfibrillar-associated protein 1	K	protein	439	Homo sapiens	P55081
WD40 repeat-containing protein SMU1	L	protein	513	Homo sapiens	Q2TAY7

31 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5O9Z_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

>5O9Z_2 116 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 3 (C), FASTA

>5O9Z_3 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 4 (D), FASTA

>5O9Z_4 U5 small nuclear ribonucleoprotein 40 kDa protein (chains D)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 5 (E), FASTA

>5O9Z_5 U4/U6 small nuclear ribonucleoprotein Prp3 (chains E)
MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTL
RFVDKLFEAVEEGRSSRHSKSSSDRSRKRELKEVFGDDSEISKESSGVKKRRIPRFEEVE
EEPEVIPGPPSESPGMLTKLQIKQMMEAATRQIEERKKQLSFISPPTPQPKTPSSSQPER
LPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLIGNANMVGLANLHAMGI
APPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVKREQFKQQLKEK
PSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKLQAEISQAAR
KTGIHTSTRLALIAPKKELKEGDIPEIEWWDSYIIPNGFDLTEENPKREDYFGITNLVEH
PAQLNPPVDNDTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRISN
LMRVLGTEAVQDPTKVEAHVRAQMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQG
VHISVYRVRNLSNPAKKFKIEANAGQLYLTGVVVLHKDVNVVVVEGGPKAQKKFKRLMLH
RIKWDEQTSNTKGDDDEESDEEAVKKTNKCVLVWEGTAKDRSFGEMKFKQCPTENMAREH
FKKHGAEHYWDLALSESVLESTD

Sequence of entity 6 (F), FASTA

>5O9Z_6 U4/U6 small nuclear ribonucleoprotein Prp4 (chains F)
MASSRASSTATKTKAPDDLVAPVVKKPHIYYGSLEEKERERLAKGESGILGKDGLKAGIE
AGNINITSGEVFEIEEHISERQAEVLAEFERRKRARQINVSTDDSEVKACLRALGEPITL
FGEGPAERRERLRNILSVVGTDALKKTKKDDEKSKKSKEEYQQTWYHEGPNSLKVARLWI
ANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPISYCHFSP
NSKMLATACWSGLCKLWSVPDCNLLHTLRGHNTNVGAIVFHPKSTVSLDPKDVNLASCAA
DGSVKLWSLDSDEPVADIEGHTVRVARVMWHPSGRFLGTTCYDRSWRLWDLEAQEEILHQ
EGHSMGVYDIAFHQDGSLAGTGGLDAFGRVWDLRTGRCIMFLEGHLKEIYGINFSPNGYH
IATGSGDNTCKVWDLRQRRCVYTIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWTHPG
WSPLKTLAGHEGKVMGLDISSDGQLIATCSYDRTFKLWMAE

Sequence of entity 7 (G), FASTA

>5O9Z_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

>5O9Z_8 U4/U6 small nuclear ribonucleoprotein Prp31 (chains H)
MSLADELLADLEEAAEEEEGGSYGEEEEEPAIEDVQEETQLDLSGDSVKTIAKLWDSKMF
AEIMMKIEEYISKQAKASEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSK
RFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLS
EEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTN
LSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCT
LAARVDSFHESTEGKVGYELKDEIERKFDKWQEPPPVKQVKPLPAPLDGQRKKRGGRRYR
KMKERLGLTEIRKQANRMSFGEIEEDAYQEDLGFSLGHLGKSGSGRVRQTQVNEATKARI
SKTLQRTLQKQSVVYGGKSTIRDRSSGTASSVAFTPLQGLEIVNPQAAEKKVAEANQKYF
SSMAEFLKVKGEKSGLMST

Sequence of entity 9 (I), FASTA

>5O9Z_9 Pre-mRNA-splicing factor 38A (chains I)
MANRTVKDAHSIHGTNPQYLVEKIIRTRIYESKYWKEECFGLTAELVVDKAMELRFVGGV
YGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYL
EPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVLEEAEQLEPR
VSALEEDMDDVESSEEEEEEDEKLERVPSPDHRRRSYRDLDKPRRSPTLRYRRSRSRSPR
RRSRSPKRRSPSPRRERHRSKSPRRHRSRSRDRRHRSRSKSPGHHRSHRHRSHSKSPERS
KKSHKKSRRGNE

Sequence of entity 10 (J), FASTA

>5O9Z_10 Thioredoxin-like protein 4A (chains J)
MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYL
VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVY
RGARKGRGLVVSPKDYSTKYRY

Sequence of entity 11 (K), FASTA

>5O9Z_11 Microfibrillar-associated protein 1 (chains K)
MSVPSALMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEF
QFIKKAKEQEAEPEEQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEV
EGDAWRMEREDSSEEEEEEIDDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESE
SESEYEEYTDSEDEMEPRLKPVFIRKKDRVTVQEREAEALKQKELEQEAKRMAEERRKYT
LKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWKVRELKRIKRDREDREALEKE
KAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFFMDEDEEVYKRDF
SAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQK
AAGVRDVFERPSAKKRKTT

Sequence of entity 12 (L), FASTA

>5O9Z_12 WD40 repeat-containing protein SMU1 (chains L)
MSIEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVL
QAIQSLKLPDKTLIDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENL
LARSYFDPREAYPDGSSKEKRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPP
GMTIDLFRGKAAVKDVEEEKFPTQLSRHIKFGQKSHVECARFSPDGQYLVTGSVDGFIEV
WNFTTGKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLATGAQDGKIKVWKIQSGQCLR
RFERAHSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGKTLKEFRGHSSFVNEATFTQD
GHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNRSN
TVVIMNMQGQIVRSFSSGKREGGDFVCCALSPRGEWIYCVGEDFVLYCFSTVTGKLERTL
TVHEKDVIGIAHHPHQNLIATYSEDGLLKLWKP

Primary citation

Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. Bertram, K., Agafonov, D.E., Dybkov, O. et al. Cell (2017) 170:701-713.e11. DOI 10.1016/j.cell.2017.07.011 · 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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