8Q7X: Recycling U5 snRNP

Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 4). Determined by electron microscopy at 4.6 Å resolution. Released 17 Apr 2024.

Method: Electron microscopy
Resolution: 4.6 Å
Organism: Homo sapiens
Chains: 15
Atoms: 41,355
Mol. weight: 1040.74 kDa
Ligands: GTP, MG
Released: 17 Apr 2024

Explore 8Q7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q7X contains 290 α-helices and 251 β-strands across 14 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	14-19	6	59
β-strand	24-32	9	59
β-strand	38-46	9	59
β-strand	52-60	9	59
β-strand	65-69	5	59
α-helix	76-78	3

Chain A: 90 helices, 61 β-strands

Element	Residues	Length	Sheet
α-helix	28-44	17
α-helix	63-72	10
α-helix	86-90	5
α-helix	91-94	4
α-helix	95-103	9
α-helix	106-108	3
β-strand	115-121	7	1
β-strand	127	1	1
β-strand	134-135	2	2
α-helix	137-157	21
α-helix	163-165	3
α-helix	174-177	4
α-helix	178-181	4
α-helix	185-187	3
β-strand	220	1	3
β-strand	227-229	3	3
α-helix	232-241	10
α-helix	260-269	10
α-helix	310-315	6
α-helix	329-331	3
α-helix	357-361	5
α-helix	371-373	3
α-helix	398-403	6
α-helix	407-408	2
β-strand	415-417	3	3
β-strand	419-420	2	2
α-helix	421-423	3
α-helix	428-433	6
α-helix	435-436	2
α-helix	441-459	19
α-helix	463-466	4
α-helix	472-477	6
β-strand	482-488	7	1
α-helix	489-508	20
β-strand	516-518	3	4
β-strand	524-526	3	4
α-helix	532-536	5
α-helix	542-564	23
α-helix	571-583	13
α-helix	585-588	4
α-helix	599-616	18
α-helix	631-656	26
α-helix	680-694	15
α-helix	699-705	7
α-helix	709-721	13
α-helix	724-726	3
α-helix	733-762	30
α-helix	769-797	29
α-helix	803-820	18
α-helix	822-827	6
α-helix	835-849	15
α-helix	858-872	15
α-helix	874-886	13
α-helix	892-893	2
β-strand	894-899	6	5
β-strand	906-910	5	5
α-helix	913-932	20
β-strand	940	1	6
α-helix	948-960	13
β-strand	973-980	8	6
β-strand	982	1	7
α-helix	990-997	8
α-helix	1003-1011	9
β-strand	1016-1019	4	5
β-strand	1022-1025	4	5
α-helix	1037-1052	16
α-helix	1055-1062	8
α-helix	1068-1070	3
α-helix	1078-1081	4
β-strand	1085-1090	6	6
β-strand	1094-1101	8	6
α-helix	1103-1116	14
α-helix	1144-1158	15
β-strand	1167	1	7
α-helix	1170-1172	3
β-strand	1174-1178	5	6
β-strand	1185-1189	5	8
β-strand	1192-1198	7	8
β-strand	1213-1217	5	8
β-strand	1224-1232	9	8
α-helix	1234-1247	14
α-helix	1256-1271	16
α-helix	1277-1280	4
α-helix	1283-1303	21
α-helix	1307-1308	2
α-helix	1313-1315	3
α-helix	1320-1322	3
β-strand	1332	1	9
β-strand	1334	1	10
β-strand	1341-1346	6	11
β-strand	1349-1354	6	11
β-strand	1364	1	10
α-helix	1369-1371	3
α-helix	1375-1398	24
α-helix	1419-1423	5
α-helix	1427-1430	4
α-helix	1436-1441	6
α-helix	1442-1445	4
α-helix	1458-1461	4
α-helix	1468-1477	10
α-helix	1481-1484	4
β-strand	1502-1503	2	12
α-helix	1531-1537	7
α-helix	1539-1542	4
β-strand	1552-1555	4	13
α-helix	1560	1
β-strand	1561-1563	3	13
α-helix	1567-1576	10
α-helix	1581-1598	18
β-strand	1606-1611	6	14
β-strand	1626	1	15
β-strand	1629-1637	9	14
β-strand	1640	1	16
β-strand	1643-1644	2	14
β-strand	1652	1	16
β-strand	1657-1667	11	14
α-helix	1676-1687	12
β-strand	1694	1	15
β-strand	1700-1706	7	14
β-strand	1711-1716	6	14
α-helix	1723-1736	14
α-helix	1738-1751	14
β-strand	1753-1754	2	12
α-helix	2072-2080	9
α-helix	2083-2085	3
β-strand	2090-2092	3	17
β-strand	2097	1	17
β-strand	2103-2107	5	17
α-helix	2108-2116	9
α-helix	2123-2124	2
β-strand	2125-2131	7	17
β-strand	2139-2147	9	17
β-strand	2150	1	18
β-strand	2151-2152	2	19
β-strand	2157-2158	2	19
α-helix	2163-2164	2
β-strand	2173-2181	9	17
α-helix	2190-2202	13
β-strand	2212-2217	6	17
β-strand	2223-2230	8	17
α-helix	2232-2240	9
β-strand	2256-2258	3	17
β-strand	2260-2264	5	17
β-strand	2270-2272	3	17
β-strand	2273-2274	2	20
β-strand	2280	1	18
α-helix	2285-2287	3
β-strand	2296-2297	2	20
α-helix	2300-2303	4
α-helix	2311-2315	5
α-helix	2317-2319	3

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-21	6	59
β-strand	26-33	8	59
β-strand	40-48	9	59
β-strand	64-72	9	59
α-helix	74-76	3
β-strand	77-84	8	59
α-helix	85-87	3

Chain B: 97 helices, 66 β-strands

Element	Residues	Length	Sheet
α-helix	40	1
β-strand	41	1	9
α-helix	42	1
α-helix	59-62	4
α-helix	419-421	3
β-strand	436-438	3	21
β-strand	442-447	6	21
α-helix	450-456	7
β-strand	463	1	22
β-strand	480	1	22
α-helix	483-487	5
α-helix	489-492	4
β-strand	499-502	4	23
α-helix	510-521	12
α-helix	533-535	3
β-strand	537-541	5	23
α-helix	545-558	14
β-strand	566-568	3	23
α-helix	573-582	10
β-strand	585-588	4	23
α-helix	590-599	10
α-helix	603-605	3
β-strand	609-614	6	23
α-helix	617-620	4
α-helix	625-642	18
β-strand	647-652	6	23
α-helix	658-664	7
β-strand	673-675	3	23
α-helix	678-680	3
β-strand	685-692	8	21
α-helix	697-714	18
β-strand	721-724	4	21
α-helix	728-744	17
α-helix	748-750	3
α-helix	757-767	11
α-helix	774-777	4
β-strand	782-785	4	21
α-helix	791-802	12
β-strand	808-811	4	21
α-helix	813-818	6
β-strand	823	1	24
β-strand	825-829	5	21
β-strand	832-835	4	25
β-strand	840-843	4	25
α-helix	844-845	2
α-helix	846-852	7
β-strand	856	1	24
β-strand	865-872	8	21
α-helix	876-882	7
α-helix	897-906	10
β-strand	912	1	26
α-helix	913-920	8
α-helix	924-931	8
α-helix	934-936	3
α-helix	940-944	5
α-helix	950-966	17
β-strand	970-972	3	27
β-strand	978	1	26
β-strand	979-981	3	27
α-helix	983-990	8
α-helix	995-1004	10
α-helix	1011-1019	9
α-helix	1022-1024	3
α-helix	1031-1033	3
α-helix	1034-1041	8
α-helix	1055-1067	13
α-helix	1070-1072	3
α-helix	1075-1102	28
α-helix	1105-1120	16
α-helix	1128-1130	3
α-helix	1137-1145	9
α-helix	1150-1154	5
α-helix	1158-1164	7
α-helix	1171-1179	9
β-strand	1184-1192	9	28
β-strand	1197-1206	10	28
β-strand	1218-1226	9	29
β-strand	1233-1242	10	29
α-helix	1243-1245	3
β-strand	1250-1257	8	28
β-strand	1265-1272	8	29
β-strand	1279-1285	7	29
α-helix	1291-1293	3
α-helix	1295-1300	6
α-helix	1304-1306	3
β-strand	1308	1	30
α-helix	1309-1311	3
α-helix	1315-1318	4
β-strand	1327	1	30
α-helix	1330-1339	10
β-strand	1346-1349	4	31
α-helix	1356-1370	15
β-strand	1376-1379	4	31
α-helix	1383-1393	11
α-helix	1394-1398	5
α-helix	1403-1404	2
β-strand	1405-1407	3	31
α-helix	1412-1421	10
β-strand	1424-1427	4	31
α-helix	1429-1436	8
α-helix	1443-1446	4
β-strand	1450-1453	4	31
α-helix	1456-1460	5
α-helix	1465-1478	14
β-strand	1486-1491	6	31
α-helix	1493	1
β-strand	1494	1	32
α-helix	1497-1503	7
β-strand	1511-1513	3	31
α-helix	1516-1518	3
α-helix	1522	1
β-strand	1523-1530	8	33
α-helix	1535-1541	7
α-helix	1543-1553	11
β-strand	1559-1563	5	33
α-helix	1568-1582	15
β-strand	1590	1	34
α-helix	1598-1601	4
α-helix	1607-1613	7
β-strand	1617-1620	4	33
α-helix	1626-1637	12
β-strand	1641	1	34
β-strand	1643-1647	5	33
α-helix	1648-1650	3
β-strand	1660-1664	5	33
β-strand	1667-1670	4	35
β-strand	1675-1678	4	35
α-helix	1679-1680	2
α-helix	1681-1689	9
β-strand	1700-1707	8	33
α-helix	1708-1710	3
α-helix	1711-1717	7
α-helix	1721	1
β-strand	1722	1	32
α-helix	1733-1741	9
β-strand	1747	1	36
α-helix	1748-1755	8
α-helix	1759-1764	6
α-helix	1768-1771	4
α-helix	1778-1798	21
β-strand	1802-1805	4	36
β-strand	1809-1812	4	36
α-helix	1814-1821	8
α-helix	1826-1835	10
α-helix	1842-1850	9
α-helix	1853-1855	3
α-helix	1865-1871	7
α-helix	1887-1899	13
α-helix	1906-1933	28
α-helix	1936-1951	16
α-helix	1968-1975	8
α-helix	1983-1986	4
α-helix	1990-1994	5
α-helix	2003-2013	11
β-strand	2017-2018	2	37
β-strand	2021-2022	2	38
β-strand	2034-2040	7	38
β-strand	2042-2043	2	37
β-strand	2064-2070	7	39
β-strand	2076-2082	7	39
β-strand	2089-2095	7	38
β-strand	2102-2110	9	39
β-strand	2118-2124	7	39

Chain c: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	30-37	8
β-strand	42-46	5	59
β-strand	50-58	9	59
β-strand	65-76	12	59
β-strand	90-101	12	59
β-strand	108-111	4	59
α-helix	112-113	2

Chain C: 42 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	116-122	7
β-strand	129-136	8	40
α-helix	143-153	11
α-helix	172-177	6
β-strand	184-191	8	40
β-strand	197-204	8	40
α-helix	213-219	7
β-strand	224-230	7	40
α-helix	237-248	12
β-strand	252-258	7	40
α-helix	262-265	4
α-helix	271-292	22
α-helix	302-304	3
β-strand	307-311	5	40
β-strand	316-318	3	40
α-helix	320-330	11
α-helix	336-339	4
α-helix	340-342	3
β-strand	348-350	3	41
β-strand	355-357	3	41
α-helix	365-367	3
α-helix	368-369	2
α-helix	370-374	5
α-helix	375-385	11
α-helix	392-399	8
α-helix	412-424	13
α-helix	428-436	9
α-helix	445-452	8
β-strand	453	1	42
α-helix	460-465	6
β-strand	475-483	9	43
β-strand	490-498	9	43
β-strand	501-502	2	44
β-strand	506-510	5	43
β-strand	522-526	5	43
β-strand	530-533	4	43
β-strand	538-541	4	43
β-strand	543-544	2	44
β-strand	549-553	5	43
β-strand	563-566	4	43
α-helix	576	1
β-strand	577	1	42
α-helix	578-580	3
β-strand	588-594	7	45
α-helix	597-599	3
α-helix	600-606	7
α-helix	610-613	4
β-strand	618-621	4	45
β-strand	627-631	5	45
α-helix	634-644	11
α-helix	645-649	5
β-strand	653-655	3	45
β-strand	659-660	2	45
α-helix	661-662	2
β-strand	663-666	4	46
β-strand	674-677	4	47
β-strand	684-691	8	47
α-helix	692-693	2
α-helix	696-701	6
α-helix	713-720	8
α-helix	726-729	4
β-strand	732-735	4	47
β-strand	743-747	5	47
α-helix	756-773	18
β-strand	784	1	46
β-strand	787-795	9	47
α-helix	800-803	4
α-helix	805-822	18
β-strand	825-838	14	46
α-helix	842-849	8
α-helix	850-852	3
β-strand	856-862	7	46
α-helix	863	1
β-strand	869-876	8	46
α-helix	883-890	8
β-strand	896-906	11	46
α-helix	907	1
α-helix	926-928	3
α-helix	929-941	13

Chain d: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-22	6	59
β-strand	27-35	9	59
β-strand	41-49	9	59
β-strand	55-63	9	59
β-strand	68-73	6	59
α-helix	75-79	5
α-helix	81-83	3

Chain D: 0 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	61-63	3	48
β-strand	69-74	6	49
β-strand	80-85	6	49
β-strand	89-94	6	49
β-strand	101-106	6	49
β-strand	112-117	6	50
β-strand	123-128	6	50
β-strand	133-137	5	50
β-strand	143-147	5	50
β-strand	154-159	6	51
β-strand	166	1	52
β-strand	167-171	5	51
β-strand	175-177	3	51
β-strand	180	1	52
β-strand	189-191	3	51
β-strand	196-201	6	53
β-strand	207-212	6	53
β-strand	216-221	6	53
β-strand	227-232	6	53
β-strand	238-243	6	54
β-strand	249-254	6	54
β-strand	258-263	6	54
β-strand	275-277	3	54
β-strand	291-293	3	55
β-strand	299-302	4	55
β-strand	309-313	5	55
β-strand	319-323	5	55
β-strand	330-335	6	48
β-strand	341-346	6	48
β-strand	350-352	3	48
β-strand	354-355	2	48

6 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
U5 snRNA	5	RNA	117	Homo sapiens
Pre-mRNA-processing-splicing factor 8	A	protein	2335	Homo sapiens	Q6P2Q9 (AlphaFold model)
U5 small nuclear ribonucleoprotein 200 kDa helicase	B	protein	2136	Homo sapiens	O75643 (AlphaFold model)
116 kDa U5 small nuclear ribonucleoprotein component	C	protein	972	Homo sapiens	Q15029 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa protein	D	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
Probable ATP-dependent RNA helicase DDX23	E	protein	820	Homo sapiens	Q9BUQ8
Pre-mRNA-processing factor 6	F	protein	941	Homo sapiens	O94906
CD2 antigen cytoplasmic tail-binding protein 2	G	protein	343	Homo sapiens	O95400
Small nuclear ribonucleoprotein Sm D1	a	protein	119	Homo sapiens	P62314
Small nuclear ribonucleoprotein-associated proteins B and B'	b	protein	240	Homo sapiens	P14678
Small nuclear ribonucleoprotein Sm D2	c	protein	118	Homo sapiens	P62316
Small nuclear ribonucleoprotein Sm D3	d	protein	126	Homo sapiens	P62318

3 more molecules are not listed.

Sequence of entity 1 (5), FASTA

>8Q7X_1 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 2 (A), FASTA

>8Q7X_2 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 3 (B), FASTA

>8Q7X_3 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains B)
MADVTARSLQYEYKANSNLVLQADRSLIDRTRRDEPTGEVLSLVGKLEGTRMGDKAQRTK
PQMQEERRAKRRKRDEDRHDINKMKGYTLLSEGIDEMVGIIYKPKTKETRETYEVLLSFI
QAALGDQPRDILCGAADEVLAVLKNEKLRDKERRKEIDLLLGQTDDTRYHVLVNLGKKIT
DYGGDKEIQNMDDNIDETYGVNVQFESDEEEGDEDVYGEVREEASDDDMEGDEAVVRCTL
SANLVASGELMSSKKKDLHPRDIDAFWLQRQLSRFYDDAIVSQKKADEVLEILKTASDDR
ECENQLVLLLGFNTFDFIKVLRQHRMMILYCTLLASAQSEAEKERIMGKMEADPELSKFL
YQLHETEKEDLIREERSRRERVRQSRMDTDLETMDLDQGGEALAPRQVLDLEDLVFTQGS
HFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKT
LNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIY
IAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKG
GERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYED
VATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQ
VLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPY
GFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGR
WTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDM
LNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTA
ALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSL
SSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMAD
MVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVV
KKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKV
ELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFE
PLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESL
YQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYIT
PMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWK
QRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDV
AHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVI
VFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYL
HEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYP
IYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEI
VTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSK
CISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPI
RHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAI
RLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVE
SVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQ
LEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATG
AHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD

Sequence of entity 4 (C), FASTA

>8Q7X_4 116 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 5 (D), FASTA

>8Q7X_5 U5 small nuclear ribonucleoprotein 40 kDa protein (chains D)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 6 (E), FASTA

>8Q7X_6 Probable ATP-dependent RNA helicase DDX23 (chains E)
MAGELADKKDRDASPSKEERKRSRTPDRERDRDRDRKSSPSKDRKRHRSRDRRRGGSRSR
SRSRSKSAERERRHKERERDKERDRNKKDRDRDKDGHRRDKDRKRSSLSPGRGKDFKSRK
DRDSKKDEEDEHGDKKPKAQPLSLEELLAKKKAEEEAEAKPKFLSKAEREAEALKRRQQE
VEERQRMLEEERKKRKQFQDLGRKMLEDPQERERRERRERMERETNGNEDEEGRQKIREE
KDKSKELHAIKERYLGGIKKRRRTRHLNDRKFVFEWDASEDTSIDYNPLYKERHQVQLLG
RGFIAGIDLKQQKREQSRFYGDLMEKRRTLEEKEQEEARLRKLRKKEAKQRWDDRHWSQK
KLDEMTDRDWRIFREDYSITTKGGKIPNPIRSWKDSSLPPHILEVIDKCGYKEPTPIQRQ
AIPIGLQNRDIIGVAETGSGKTAAFLIPLLVWITTLPKIDRIEESDQGPYAIILAPTREL
AQQIEEETIKFGKPLGIRTVAVIGGISREDQGFRLRMGCEIVIATPGRLIDVLENRYLVL
SRCTYVVLDEADRMIDMGFEPDVQKILEHMPVSNQKPDTDEAEDPEKMLANFESGKHKYR
QTVMFTATMPPAVERLARSYLRRPAVVYIGSAGKPHERVEQKVFLMSESEKRKKLLAILE
QGFDPPIIIFVNQKKGCDVLAKSLEKMGYNACTLHGGKGQEQREFALSNLKAGAKDILVA
TDVAGRGIDIQDVSMVVNYDMAKNIEDYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELK
QAILESPVSSCPPELANHPDAQHKPGTILTKKRREETIFA

Sequence of entity 7 (F), FASTA

>8Q7X_7 Pre-mRNA-processing factor 6 (chains F)
MNKKKKPFLGMPAPLGYVPGLGRGATGFTTRSDIGPARDANDPVDDRHAPPGKRTVGDQM
KKNQAADDDDEDLNDTNYDEFNGYAGSLFSSGPYEKDDEEADAIYAALDKRMDERRKERR
EQREKEEIEKYRMERPKIQQQFSDLKRKLAEVTEEEWLSIPEVGDARNKRQRNPRYEKLT
PVPDSFFAKHLQTGENHTSVDPRQTQFGGLNTPYPGGLNTPYPGGMTPGLMTPGTGELDM
RKIGQARNTLMDMRLSQVSDSVSGQTVVDPKGYLTDLNSMIPTHGGDINDIKKARLLLKS
VRETNPHHPPAWIASARLEEVTGKLQVARNLIMKGTEMCPKSEDVWLEAARLQPGDTAKA
VVAQAVRHLPQSVRIYIRAAELETDIRAKKRVLRKALEHVPNSVRLWKAAVELEEPEDAR
IMLSRAVECCPTSVELWLALARLETYENARKVLNKARENIPTDRHIWITAAKLEEANGNT
QMVEKIIDRAITSLRANGVEINREQWIQDAEECDRAGSVATCQAVMRAVIGIGIEEEDRK
HTWMEDADSCVAHNALECARAIYAYALQVFPSKKSVWLRAAYFEKNHGTRESLEALLQRA
VAHCPKAEVLWLMGAKSKWLAGDVPAARSILALAFQANPNSEEIWLAAVKLESENDEYER
ARRLLAKARSSAPTARVFMKSVKLEWVQDNIRAAQDLCEEALRHYEDFPKLWMMKGQIEE
QKEMMEKAREAYNQGLKKCPHSTPLWLLLSRLEEKIGQLTRARAILEKSRLKNPKNPGLW
LESVRLEYRAGLKNIANTLMAKALQECPNSGILWSEAIFLEARPQRRTKSVDALKKCEHD
PHVLLAVAKLFWSQRKITKAREWFHRTVKIDSDLGDAWAFFYKFELQHGTEEQQEEVRKR
CESAEPRHGELWCAVSKDIANWQKKIGDILRLVAGRIKNTF

Sequence of entity 8 (G), FASTA

>8Q7X_8 CD2 antigen cytoplasmic tail-binding protein 2 (chains G)
GPMPKRKVTFQGVGDEEDEDEIIVPKKKLVDPVAGSGGPGSRFKGKHSLDSDEEEDDDDG
GSSKYDILASEDVEGQEAATLPSEGGVRITPFNLQEEMEEGHFDADGNYFLNRDAQIRDS
WLDNIDWVKIRERPPGQRQASDSEEEDSLGQTSMSAQALLEGLLELLLPRETVAGALRRL
GARGGGKGRKGPGQPSSPQRLDRLSGLADQMVARGNLGVYQETRERLAMRLKGLGCQTLG
PHNPTPPPSLDMFAEELAEEELETPTPTQRGEAESRGDGLVDVMWEYKWENTGDAELYGP
FTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT

Sequence of entity 9 (a), FASTA

>8Q7X_9 Small nuclear ribonucleoprotein Sm D1 (chains a)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Sequence of entity 10 (b), FASTA

>8Q7X_10 Small nuclear ribonucleoprotein-associated proteins B and B' (chains b)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGPPPPGMRPPRP

Sequence of entity 11 (c), FASTA

>8Q7X_11 Small nuclear ribonucleoprotein Sm D2 (chains c)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Sequence of entity 12 (d), FASTA

>8Q7X_12 Small nuclear ribonucleoprotein Sm D3 (chains d)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Structural basis of human U5 snRNP late biogenesis and recycling. Riabov Bassat, D., Visanpattanasin, S., Vorlander, M.K. et al. Nat Struct Mol Biol (2024) 31:747-751. DOI 10.1038/s41594-024-01243-4 · 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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