5YZG: Human Catalytic Step I Spliceosome

The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution. Determined by electron microscopy at 4.1 Å resolution. Released 8 Aug 2018.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 55
Atoms: 103,906
Mol. weight: 3193.82 kDa
Ligands: IHP, GTP, MG, ADP
Released: 8 Aug 2018

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

Secondary structure: helices and β-sheets

5YZG contains 684 α-helices and 602 β-strands across 51 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 1: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	143
α-helix	19-26	8
α-helix	27-29	3
β-strand	32-36	5	143
β-strand	39-40	2	144
β-strand	45-46	2	144
β-strand	49-54	6	143
α-helix	57-67	11
β-strand	71-72	2	145
β-strand	75-76	2	145
β-strand	78-81	4	143
β-strand	141-148	8	146
β-strand	151-160	10	146
α-helix	166-177	12
β-strand	188-193	6	146
β-strand	197-200	4	146
β-strand	213	1	147
β-strand	216	1	147
β-strand	219	1	148
β-strand	233-236	4	146
β-strand	244	1	148
β-strand	248-251	4	146
α-helix	256-258	3
β-strand	264-270	7	146
α-helix	272-279	8
β-strand	292-299	8	146

Chain 2: 5 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	103-104	2	29
β-strand	115-120	6	30
β-strand	134-138	5	30
β-strand	149-154	6	30
β-strand	159-165	7	30
β-strand	172-175	4	31
β-strand	182-185	4	31
β-strand	198-201	4	31
β-strand	214-218	5	31
β-strand	232-235	4	32
β-strand	242-245	4	32
β-strand	250-252	3	32
β-strand	264-265	2	32
β-strand	275-278	4	33
β-strand	284-288	5	33
β-strand	294-298	5	33
β-strand	303-308	6	33
β-strand	319-322	4	34
β-strand	328-332	5	34
β-strand	336-341	6	34
β-strand	346-352	7	34
β-strand	363-368	6	35
β-strand	377-382	6	35
β-strand	385-389	5	35
β-strand	397-399	3	35
β-strand	406-411	6	29
α-helix	412	1
α-helix	413-415	3
β-strand	418-422	5	29
β-strand	430-432	3	29
β-strand	493-498	6	36
β-strand	501-507	7	36
α-helix	513-524	12
β-strand	532	1	37
β-strand	535-537	3	36
β-strand	541-544	4	36
β-strand	562	1	38
β-strand	577-580	4	36
β-strand	588	1	38
β-strand	592-595	4	36
α-helix	600-602	3
β-strand	608-614	7	36
α-helix	616-623	8
β-strand	627	1	39
β-strand	634	1	39
β-strand	639	1	37
β-strand	640-645	6	36

Chain 3: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	42
β-strand	19-28	10	42
α-helix	34-45	12
β-strand	50	1	43
β-strand	57	1	43
β-strand	65-69	5	42
β-strand	73-76	4	42
β-strand	95	1	44
β-strand	109-112	4	42
β-strand	120	1	44
β-strand	124-127	4	42
α-helix	132-134	3
β-strand	140-146	7	42
α-helix	148-155	8
β-strand	159	1	45
β-strand	165	1	45
β-strand	169-176	8	42

Chain 4: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	15-20	6
β-strand	27	1	12
α-helix	31-37	7

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

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	17-22	6	111
β-strand	27-35	9	111
β-strand	41-49	9	111
β-strand	55-63	9	111
α-helix	65-67	3
β-strand	68-73	6	111

Chain A: 115 helices, 63 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
α-helix	63-72	10
α-helix	84-91	8
α-helix	92-94	3
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	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	334-337	4
α-helix	340-342	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	532-538	7
α-helix	542-566	25
α-helix	571-583	13
α-helix	585-588	4
α-helix	591-594	4
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	835-852	18
α-helix	858-872	15
α-helix	874-886	13
β-strand	894-900	7	7
β-strand	905-910	6	7
α-helix	913-933	21
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	1275-1280	6
α-helix	1282-1301	20
α-helix	1308-1310	3
α-helix	1314-1317	4
α-helix	1320-1322	3
α-helix	1334	1
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
β-strand	1501-1503	3	12
α-helix	1508-1516	9
α-helix	1523-1525	3
α-helix	1531-1537	7
α-helix	1539-1542	4
β-strand	1552-1554	3	13
β-strand	1561-1563	3	13
α-helix	1567-1576	10
α-helix	1581-1598	18
β-strand	1606-1611	6	14
α-helix	1612-1615	4
β-strand	1629-1639	11	14
α-helix	1640-1642	3
β-strand	1643-1644	2	14
α-helix	1652-1654	3
β-strand	1655-1667	13	14
α-helix	1676-1689	14
β-strand	1700-1706	7	14
β-strand	1711-1716	6	14
α-helix	1722-1734	13
α-helix	1738-1750	13
β-strand	1753-1755	3	12
α-helix	1767-1769	3
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

Chain b: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	16-21	6	111
β-strand	26-33	8	111
β-strand	40-48	9	111
β-strand	64-72	9	111
α-helix	74-76	3
β-strand	77-84	8	111
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	111
β-strand	24-32	9	111
β-strand	38-46	9	111
β-strand	53-60	8	111
α-helix	62-64	3
β-strand	65-69	5	111
α-helix	70-71	2
α-helix	76-79	4

39 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	Homo sapiens
U2 snRNA	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

33 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5YZG_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

>5YZG_2 U5 snRNA (chains B)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 3 (C), FASTA

>5YZG_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

>5YZG_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

>5YZG_5 U5 small nuclear ribonucleoprotein 40 kDa protein (chains E)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 6 (F), FASTA

>5YZG_6 U6 snRNA (chains F)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUUU

Sequence of entity 7 (G), FASTA

>5YZG_7 Pre-mRNA (chains G)
GGGAAUACACGGAAUUCGAGCUCGCCCACUCUUGGAUCGGAAACCCGUCGGCCUCCGAAC
GNGUAAGAGCCUAGCAUGUAGAACUGGUUACCUGCAGCCCAAGCUUGCGUACACCAUCAG
GGUACGUACUAGUACGUACACCAUCAGGGUACGGCUGCACGUCUAGGGCGCAGUAGUCCA
GGGUUUCCUUGAUGAUGUCAUACUUAUCCUGUCCCUUUUUUUUCCACGGCUCGCGGUUGA
GGACAAACUCUUCGCGGUCUUUCCAGUGGGGAUCC

Sequence of entity 8 (H), FASTA

>5YZG_8 U2 snRNA (chains H)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC

Sequence of entity 9 (I), FASTA

>5YZG_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

>5YZG_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

>5YZG_11 Pre-mRNA-splicing factor SPF27 (chains K)
MAGTGLVAGEVVVDALPYFDQGYEAPGVREAAAALVEEETRRYRPTKNYLSYLTAPDYSA
FETDIMRNEFERLAARQPIELLSMKRYELPAPSSGQKNDITAWQECVNNSMAQLEHQAVR
IENLELMSQHGCNAWKVYNENLVHMIEHAQKELQKLRKHIQDLNWQRKNMQLTAGSKLRE
MESNWVSLVSKNYEIERTIVQLENEIYQIKQQHGEANKENIRQDF

Sequence of entity 12 (L), FASTA

>5YZG_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	7
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ZN	Zinc ion	Zn	7
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Structure of a human catalytic step I spliceosome. Zhan, X., Yan, C., Zhang, X. et al. Science (2018) 359:537-545. DOI 10.1126/science.aar6401 · 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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