6ID1: Pre-mRNA-processing-splicing factor 8

Name: PDB 6ID1: Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution
Published: 2019-03-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: splicing

Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution. Determined by electron microscopy at 2.86 Å resolution. Released 13 Mar 2019.

Method: Electron microscopy
Resolution: 2.86 Å
Organism: Homo sapiens
Chains: 43
Atoms: 79,882
Mol. weight: 2147.52 kDa
Ligands: IHP, GTP, MG, ZN
Released: 13 Mar 2019

Explore 6ID1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ID1 contains 495 α-helices and 372 β-strands across 39 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	88
β-strand	27-35	9	88
β-strand	41-49	9	88
β-strand	55-63	9	88
α-helix	65-67	3
β-strand	68-73	6	88

Chain A: 94 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
α-helix	47-49	3
α-helix	54-58	5
α-helix	60-62	3
α-helix	63-72	10
α-helix	82-84	3
α-helix	85-91	7
α-helix	92-94	3
α-helix	95-104	10
β-strand	115-121	7	1
β-strand	127-129	3	1
β-strand	134	1	2
α-helix	137-156	20
α-helix	162-165	4
α-helix	173-177	5
α-helix	178-181	4
α-helix	194-196	3
β-strand	220	1	3
β-strand	227-229	3	3
α-helix	232-241	10
α-helix	252-255	4
α-helix	260-268	9
α-helix	312-315	4
α-helix	357-358	2
β-strand	379	1	4
α-helix	398-405	8
β-strand	415-417	3	3
β-strand	420	1	2
α-helix	428-432	5
α-helix	434-436	3
α-helix	441-459	19
α-helix	472-476	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	532-537	6
α-helix	542-565	24
α-helix	572-583	12
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	677-696	20
α-helix	706-721	16
α-helix	724-726	3
α-helix	733-763	31
α-helix	769-796	28
α-helix	804-819	16
α-helix	822-824	3
β-strand	825	1	6
α-helix	827-829	3
α-helix	835-847	13
α-helix	849-851	3
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	972-980	9	8
α-helix	990-1000	11
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	1077-1080	4
β-strand	1085-1091	7	8
β-strand	1094-1102	9	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	1185-1188	4	9
β-strand	1192-1198	7	9
β-strand	1213-1217	5	9
α-helix	1218	1
β-strand	1224-1232	9	9
α-helix	1234-1248	15
α-helix	1258-1273	16
α-helix	1282-1303	22
α-helix	1314-1317	4
α-helix	1320-1322	3
α-helix	1337-1339	3
β-strand	1341-1345	5	10
β-strand	1350-1354	5	10
α-helix	1375-1398	24
α-helix	1405-1410	6
α-helix	1419-1423	5
α-helix	1430-1432	3
α-helix	1436-1441	6
α-helix	1469-1478	10
α-helix	1480-1485	6
α-helix	1490-1493	4
β-strand	1501-1503	3	11
α-helix	1512-1515	4
α-helix	1520-1522	3
α-helix	1529-1531	3
α-helix	1532-1537	6
α-helix	1539-1542	4
β-strand	1553-1554	2	12
α-helix	1555	1
β-strand	1561-1562	2	12
α-helix	1569-1576	8
α-helix	1581-1597	17
α-helix	1601-1603	3
β-strand	1610	1	13
β-strand	1629-1631	3	13
β-strand	1642-1644	3	13
β-strand	1660-1667	8	13
α-helix	1676-1687	12
β-strand	1701-1706	6	13
β-strand	1711-1717	7	13
α-helix	1723-1733	11
α-helix	1738-1751	14
β-strand	1753-1755	3	11
α-helix	1768-1772	5
β-strand	1777-1781	5	14
β-strand	1788-1792	5	15
β-strand	1798-1802	5	15
β-strand	1805-1810	6	14
β-strand	1816-1822	7	14
α-helix	1837-1851	15
β-strand	1860-1863	4	14
α-helix	1866-1868	3
α-helix	1869-1875	7
β-strand	1883-1886	4	14
α-helix	1895-1898	4
α-helix	1900-1907	8
β-strand	1914-1918	5	14
α-helix	1923-1925	3
α-helix	1929-1945	17
α-helix	1948-1954	7
α-helix	1973-1995	23
α-helix	2004-2011	8

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

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-21	6	88
β-strand	26-33	8	88
β-strand	40-48	9	88
β-strand	64-72	9	88
α-helix	74-76	3
β-strand	77-84	8	88
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	88
β-strand	24-32	9	88
β-strand	38-46	9	88
β-strand	53-60	8	88
α-helix	62-64	3
β-strand	65-69	5	88
α-helix	70-71	2
α-helix	76-79	4

Chain C: 43 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	57-59	3
α-helix	69-73	5
β-strand	78-81	4	18
α-helix	117-123	7
β-strand	129-136	8	19
α-helix	142-153	12
α-helix	174-177	4
β-strand	185-190	6	19
β-strand	198-204	7	19
α-helix	209-211	3
α-helix	212-221	10
β-strand	224-230	7	19
α-helix	237-248	12
β-strand	252-258	7	19
α-helix	261	1
α-helix	262-267	6
α-helix	271-292	22
β-strand	308-310	3	19
β-strand	318	1	19
α-helix	320-330	11
α-helix	336-341	6
β-strand	348-350	3	4
β-strand	355-357	3	4
α-helix	368-369	2
α-helix	370-374	5
α-helix	375-386	12
α-helix	392-396	5
α-helix	407-409	3
α-helix	412-424	13
α-helix	428-435	8
α-helix	445-452	8
β-strand	453	1	20
α-helix	462-467	6
β-strand	475-483	9	21
α-helix	484	1
β-strand	490-498	9	21
β-strand	501-502	2	22
β-strand	506-510	5	21
β-strand	515	1	23
β-strand	518	1	23
β-strand	523-526	4	21
β-strand	530-533	4	21
β-strand	538-540	3	21
β-strand	543-544	2	22
β-strand	549-552	4	21
β-strand	563-566	4	21
β-strand	577	1	20
α-helix	578-579	2
β-strand	588-594	7	24
α-helix	600-613	14
β-strand	618-621	4	24
β-strand	627-631	5	24
α-helix	634-643	10
α-helix	644-648	5
β-strand	653-655	3	24
β-strand	659-660	2	24
β-strand	663-666	4	25
β-strand	674-677	4	26
β-strand	684-690	7	26
α-helix	691-693	3
α-helix	694-700	7
α-helix	711-722	12
α-helix	726-729	4
β-strand	743-747	5	26
α-helix	752-754	3
α-helix	756-776	21
β-strand	783-784	2	25
β-strand	787-795	9	26
α-helix	804-821	18
β-strand	825-838	14	25
α-helix	840-851	12
β-strand	857-859	3	25
α-helix	861	1
β-strand	862	1	25
α-helix	863	1
β-strand	869-876	8	25
α-helix	883-890	8
β-strand	896-906	11	25
α-helix	916-919	4
α-helix	923-924	2
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	88
β-strand	51-59	9	88
β-strand	65-76	12	88
β-strand	90-101	12	88
α-helix	103-105	3
β-strand	106-111	6	88

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

Element	Residues	Length	Sheet
α-helix	17-27	11
β-strand	30-35	6	88
β-strand	38-50	13	88
β-strand	56-65	10	88
β-strand	70-79	10	88
α-helix	81-83	3
β-strand	84-90	7	88

Chain E: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	62-63	2	27
β-strand	71-74	4	28
β-strand	80-84	5	28
β-strand	90-94	5	28
β-strand	101-104	4	28
β-strand	114-115	2	29
β-strand	123-127	5	29
β-strand	133-137	5	29
β-strand	143-147	5	29
β-strand	154-159	6	30
α-helix	165	1
β-strand	167-171	5	30
β-strand	175-179	5	30
β-strand	186-191	6	30
β-strand	196-201	6	31
β-strand	207-212	6	31
β-strand	217-221	5	31
β-strand	227-231	5	31
β-strand	238-243	6	32
β-strand	249-254	6	32
β-strand	259-263	5	32
β-strand	275-277	3	32
β-strand	291-293	3	33
β-strand	299-302	4	33
β-strand	309-313	5	33
β-strand	319-323	5	33
β-strand	330-335	6	27
β-strand	341-346	6	27
β-strand	350-355	6	27

26 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)
U5snRNA	B	RNA	117	Homo sapiens
116 kDa U5 small nuclear ribonucleoprotein component	C	protein	972	Homo sapiens	Q15029 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa protein	E	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
U6snRNA	F	RNA	107	Homo sapiens
Crooked neck-like protein 1	J	protein	848	Homo sapiens	Q9BZJ0 (AlphaFold model)
Cell division cycle 5-like protein	L	protein	802	Homo sapiens	Q99459
Pre-mRNA-splicing factor SYF2	M	protein	243	Homo sapiens	O95926
Protein BUD31 homolog	N	protein	144	Homo sapiens	P41223
Pre-mRNA-splicing factor RBM22	O	protein	420	Homo sapiens	Q9NW64
Spliceosome-associated protein CWC15 homolog	P	protein	229	Homo sapiens	Q9P013
SNW domain-containing protein 1	R	protein	536	Homo sapiens	Q13573

21 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6ID1_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

>6ID1_2 U5snRNA (chains B)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 3 (C), FASTA

>6ID1_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 (E), FASTA

>6ID1_4 U5 small nuclear ribonucleoprotein 40 kDa protein (chains E)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 5 (F), FASTA

>6ID1_5 U6snRNA (chains F)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUUU

Sequence of entity 6 (J), FASTA

>6ID1_6 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 7 (L), FASTA

>6ID1_7 Cell division cycle 5-like protein (chains L)
MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKK
TEWSREEEEKLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKAAQRDNEEETTDDP
RKLKPGEIDPNPETKPARPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEAR
RLAALQKRRELRAAGIEIQKKRKRKRGVDYNAEIPFEKKPALGFYDTSEENYQALDADFR
KLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAILQTSGVSEFTKKRSKLVLPAP
QISDAELQEVVKVGQASEIARQTAEESGITNSASSTLLSEYNVTNNSVALRTPRTPASQD
RILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
EGLTPRSGTTPKPVINSTPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGL
LGLPAPKNDFEIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKA
VQKDLPRPSEVNETILRPLNVEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPSGNKKG
KTVGFGTNNSEHITYLEHNPYEKFSKEELKKAQDVLVQEMEVVKQGMSHGELSSEAYNQV
WEECYSQVLYLPGQSRYTRANLASKKDRIESLEKRLEINRGHMTTEAKRAAKMEKKMKIL
LGGYQSRAMGLMKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLECLKEDVQRQQER
EKELQHRYADLLLEKETLKSKF

Sequence of entity 8 (M), FASTA

>6ID1_8 Pre-mRNA-splicing factor SYF2 (chains M)
MAAIAASEVLVDSAEEGSLAAAAELAAQKREQRLRKFRELHLMRNEARKLNHQEVVEEDK
RLKLPANWEAKKARLEWELKEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKKRKNP
DLGFSDYAAAQLRQYHRLTKQIKPDMETYERLREKHGEEFFPTSNSLLHGTHVPSTEEID
RMVIDLEKQIEKRDKYSRRRPYNDDADIDYINERNAKFNKKAERFYGKYTAEIKQNLERG
TAV

Sequence of entity 9 (N), FASTA

>6ID1_9 Protein BUD31 homolog (chains N)
MPKVKRSRKAPPDGWELIEPTLDELDQKMREAETEPHEGKRKVESLWPIFRIHHQKTRYI
FDLFYKRKAISRELYEYCIKEGYADKNLIAKWKKQGYENLCCLRCIQTRDTNFGTNCICR
VPKSKLEVGRIIECTHCGCRGCSG

Sequence of entity 10 (O), FASTA

>6ID1_10 Pre-mRNA-splicing factor RBM22 (chains O)
MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPG
VRMRFKKTEVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQN
MEREISNSDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECP
YRHEKPTDPDDPLADQNIKDRYYGINDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLG
DTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV
KWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEASANYFNLPPSGPPAV
VNIALPPPPGIAPPPPPGFGPHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHSSP

Sequence of entity 11 (P), FASTA

>6ID1_11 Spliceosome-associated protein CWC15 homolog (chains P)
MTTAARPTFEPARGGRGKGEGDLSQLSKQYSSRDLPSHTKIKYRQTTQDAPEEVRNRDFR
RELEERERAAAREKNRDRPTREHTTSSSVSKKPRLDQIPAANLDADDPLTDEEDEDFEEE
SDDDDTAALLAELEKIKKERAEEQARKEQEQKAEEERIRMENILSGNPLLNLTGPSQPQA
NFKVKRRWDDDVVFKNCAKGVDDQKKDKRFVNDTLRSEFHKKFMEKYIK

Sequence of entity 12 (R), FASTA

>6ID1_12 SNW domain-containing protein 1 (chains R)
MALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGD
GGAFPEIHVAQYPLDMGRKKKMSNALAIQVDSEGKIKYDAIARQGQSKDKVIYSKYTDLV
PKEVMNADDPDLQRPDEEAIKEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYT
PSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKINKKIPRGPPSPPAPVMHSPSRKMTVK
EQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENFAKLAEALYIADRKARE
AVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDEIRHDRR
KERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDS
GFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSG
SDRRQRGREGPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE

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	7
ZN	Zinc ion	Zn	7

Primary citation

Structures of the human spliceosomes before and after release of the ligated exon. Zhang, X., Zhan, X., Yan, C. et al. Cell Res (2019) 29:274-285. DOI 10.1038/s41422-019-0143-x · 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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