7ABI: Human pre-Bact-2 spliceosome

Human pre-Bact-2 spliceosome. Determined by electron microscopy at 8.0 Å resolution. Released 10 Feb 2021.

Method: Electron microscopy
Resolution: 8.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 56
Atoms: 85,564
Mol. weight: 3129.43 kDa
Ligands: GTP, MG, IHP
Released: 10 Feb 2021

Explore 7ABI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ABI contains 652 α-helices and 615 β-strands across 52 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 0: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
α-helix	230-236	7
β-strand	238	1	138
β-strand	243	1	138
β-strand	252	1	139
β-strand	261	1	140
β-strand	263-264	2	141
β-strand	273	1	140
β-strand	307-314	8	139
β-strand	320-327	8	139
β-strand	368-369	2	141

Chain 1: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	37-41	5	144
α-helix	49-55	7
β-strand	64-67	4	144
β-strand	80-83	4	144
α-helix	87-96	10
β-strand	101	1	145
β-strand	106	1	145
β-strand	108-111	4	144

Chain 3: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	571-573	3
α-helix	594-615	22

Chain 4: 24 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	8-27	20
α-helix	33-58	26
α-helix	62-72	11
α-helix	79-87	9
α-helix	103-108	6
β-strand	112	1	173
β-strand	115	1	173
α-helix	119-121	3
α-helix	126-128	3
α-helix	132-134	3
α-helix	143-153	11
α-helix	160-167	8
α-helix	182-199	18
α-helix	206-219	14
α-helix	221-223	3
β-strand	284	1	174
β-strand	289	1	174
α-helix	294-300	7
α-helix	304-307	4
α-helix	318-333	16
α-helix	335-350	16
α-helix	353-361	9
α-helix	394-400	7
β-strand	406-408	3	175
β-strand	414-416	3	175
α-helix	419-426	8
α-helix	429-438	10
α-helix	452-462	11
α-helix	489-498	10

Chain 7: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	61-64	4
α-helix	65-79	15
α-helix	80-84	5
β-strand	88-90	3	169
α-helix	91-99	9
α-helix	107-109	3
α-helix	115-125	11
β-strand	128-132	5	169
β-strand	137-141	5	169
α-helix	148-178	31
β-strand	285	1	170
β-strand	286-289	4	171
α-helix	296-298	3
β-strand	301-309	9	171
β-strand	313-318	6	171
β-strand	324-328	5	171
α-helix	329-331	3
β-strand	332-334	3	171
α-helix	336-338	3
β-strand	342-345	4	172
β-strand	354-361	8	172
β-strand	366-371	6	172
β-strand	380-385	6	172
α-helix	386-388	3
β-strand	389-391	3	172
β-strand	392	1	170

Chain 8: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	115-117	3	136
α-helix	122-130	9

Chain a: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	27-37	11
β-strand	42-46	5	33
β-strand	51-56	6	33
β-strand	66-73	8	33
β-strand	93-101	9	33
β-strand	106-110	5	33

Chain A: 94 helices, 68 β-strands

Element	Residues	Length	Sheet
α-helix	65-70	6
α-helix	85-90	6
α-helix	91-93	3
α-helix	97-102	6
α-helix	106-108	3
β-strand	116-121	6	113
β-strand	127-128	2	113
α-helix	137-157	21
β-strand	228-229	2	114
α-helix	234-242	9
α-helix	253-256	4
α-helix	260-266	7
α-helix	299-301	3
α-helix	310-315	6
α-helix	334-336	3
α-helix	357-359	3
α-helix	373-377	5
α-helix	399-405	7
β-strand	415-416	2	114
α-helix	428-431	4
α-helix	441-458	18
α-helix	473-476	4
β-strand	482-487	6	113
α-helix	489-509	21
β-strand	516-517	2	115
β-strand	525-526	2	115
α-helix	535-537	3
α-helix	542-563	22
α-helix	564-568	5
α-helix	572-587	16
α-helix	598-616	19
α-helix	632-657	26
α-helix	679-695	17
α-helix	707-721	15
α-helix	734-763	30
α-helix	771-796	26
α-helix	803-820	18
α-helix	822-824	3
β-strand	825	1	116
α-helix	826	1
α-helix	835-850	16
α-helix	859-872	14
α-helix	874-887	14
α-helix	892-893	2
β-strand	894-896	3	117
β-strand	899	1	118
β-strand	905	1	165
β-strand	906	1	118
β-strand	909-910	2	117
α-helix	913-933	21
β-strand	944	1	119
β-strand	946	1	119
α-helix	949-960	12
β-strand	973-976	4	120
α-helix	990-1000	11
β-strand	1001	1	116
α-helix	1003-1011	9
β-strand	1017-1018	2	117
β-strand	1023-1024	2	117
α-helix	1037-1052	16
α-helix	1055-1062	8
α-helix	1077-1082	6
β-strand	1085-1089	5	121
β-strand	1096-1099	4	121
β-strand	1100-1101	2	120
α-helix	1103-1116	14
α-helix	1123-1125	3
α-helix	1144-1159	16
β-strand	1176-1178	3	120
β-strand	1185-1187	3	122
β-strand	1194-1198	5	122
α-helix	1199-1201	3
β-strand	1216-1218	3	122
β-strand	1223-1229	7	122
α-helix	1231-1233	3
α-helix	1234-1249	16
α-helix	1256-1270	15
α-helix	1275-1280	6
α-helix	1282-1303	22
α-helix	1313-1317	5
β-strand	1334	1	123
β-strand	1341-1342	2	124
β-strand	1345	1	125
β-strand	1350	1	125
β-strand	1353-1354	2	124
β-strand	1363	1	123
α-helix	1373-1374	2
α-helix	1375-1399	25
α-helix	1405-1409	5
α-helix	1420-1423	4
α-helix	1426-1429	4
α-helix	1430-1432	3
α-helix	1436-1446	11
α-helix	1458-1461	4
α-helix	1470-1477	8
α-helix	1480-1487	8
α-helix	1490-1493	4
α-helix	1529-1537	9
α-helix	1539-1542	4
α-helix	1567-1576	10
α-helix	1582-1597	16
β-strand	1610-1611	2	126
α-helix	1618-1620	3
β-strand	1629-1632	4	126
β-strand	1642-1644	3	127
β-strand	1659-1662	4	126
β-strand	1665-1666	2	128
α-helix	1676-1689	14
β-strand	1700-1701	2	126
β-strand	1703-1705	3	128
β-strand	1713-1714	2	128
β-strand	1715-1717	3	127
α-helix	1723-1734	12
α-helix	1738-1751	14
β-strand	1779-1781	3	129
α-helix	1782-1784	3
β-strand	1788-1790	3	130
β-strand	1800-1802	3	130
β-strand	1805-1810	6	129
β-strand	1816-1822	7	129
α-helix	1833-1850	18
β-strand	1862-1863	2	129
α-helix	1870-1875	6
β-strand	1885	1	129
α-helix	1893-1896	4
α-helix	1900-1907	8
β-strand	1914-1918	5	129
α-helix	1921-1924	4
α-helix	1929-1945	17
α-helix	1947-1954	8
β-strand	1961	1	131
α-helix	1969	1
β-strand	1970	1	131
α-helix	1973-1995	23
α-helix	2004-2012	9
α-helix	2072-2081	10
α-helix	2086-2088	3
β-strand	2090-2091	2	132
β-strand	2103-2107	5	132
α-helix	2108-2117	10
α-helix	2123-2124	2
β-strand	2125-2131	7	132
α-helix	2132-2133	2
β-strand	2139-2146	8	132
β-strand	2150	1	133
β-strand	2151-2152	2	134
β-strand	2157-2158	2	134
α-helix	2162-2164	3
β-strand	2173-2181	9	132
α-helix	2190-2202	13
β-strand	2212-2217	6	132
β-strand	2223-2228	6	132
α-helix	2232-2240	9
α-helix	2253-2255	3
β-strand	2258	1	132
β-strand	2260-2264	5	132
β-strand	2270-2271	2	132
β-strand	2273-2274	2	135
β-strand	2280	1	133
β-strand	2296-2297	2	135
α-helix	2300-2303	4
α-helix	2311-2314	4

44 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 small nuclear ribonucleoprotein 40 kDa protein	D	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
Splicing factor 3B subunit 3	E	protein	1217	Homo sapiens	Q15393 (AlphaFold model)
Small nuclear ribonucleoprotein F	b, i	protein	86	Homo sapiens	P62306 (AlphaFold model)
U2 small nuclear ribonucleoprotein A'	W	protein	255	Homo sapiens	P09661 (AlphaFold model)
Splicing factor 3B subunit 4	w	protein	424	Homo sapiens	Q15427
Small nuclear ribonucleoprotein G	d, k	protein	76	Homo sapiens	P62308
Intron-binding protein aquarius	U	protein	1485	Homo sapiens	O60306
Splicing factor 3B subunit 5	x	protein	86	Homo sapiens	Q9BWJ5
U6 snRNA	6	RNA	106	Homo sapiens
U2 small nuclear ribonucleoprotein B''	B	protein	225	Homo sapiens	P08579
Splicing factor 3B subunit 6	z	protein	125	Homo sapiens	Q9Y3B4
Ubiquitin-like protein 5	q	protein	73	Homo sapiens	Q9BZL1

37 more molecules are not listed.

Sequence of entity 1 (D), FASTA

>7ABI_1 U5 small nuclear ribonucleoprotein 40 kDa protein (chains D)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 2 (E), FASTA

>7ABI_2 Splicing factor 3B subunit 3 (chains E)
MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFG
VIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQF
LAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFENP
MFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG
GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFF
FLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQ
IAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANEDT
PQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN
ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPG
KKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQ
RSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERGSI
GFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSW
LSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFP
LQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAA
AFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTG
EDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVL
IGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQ
LIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRG
LLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDF
FQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRT
PPEVSKKLEDIRTRYAF

Sequence of entity 3 (b, i), FASTA

>7ABI_3 Small nuclear ribonucleoprotein F (chains b, i)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE

Sequence of entity 4 (W), FASTA

>7ABI_4 U2 small nuclear ribonucleoprotein A' (chains W)
MVKLTAELIEQAAQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGF
PLLRRLKTLLVNNNRICRIGEGLDQALPCLTELILTNNSLVELGDLDPLASLKSLTYLSI
LRNPVTNKKHYRLYVIYKVPQVRVLDFQKVKLKERQEAEKMFKGKRGAQLAKDIARRSKT
FNPGAGLPTDKKKGGPSPGDVEAIKNAIANASTLAEVERLKGLLQSGQIPGRERRSGPTD
DGEEEMEEDTVTNGS

Sequence of entity 5 (w), FASTA

>7ABI_5 Splicing factor 3B subunit 4 (chains w)
MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ

Sequence of entity 6 (d, k), FASTA

>7ABI_6 Small nuclear ribonucleoprotein G (chains d, k)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV

Sequence of entity 7 (U), FASTA

>7ABI_7 Intron-binding protein aquarius (chains U)
MAAPAQPKKIVAPTVSQINAEFVTQLACKYWAPHIKKKSPFDIKVIEDIYEKEIVKSRFA
IRKIMLLEFSQYLENYLWMNYSPEVSSKAYLMSICCMVNEKFRENVPAWEIFKKKPDHFP
FFFKHILKAALAETDGEFSLHEQTVLLLFLDHCFNSLEVDLIRSQVQQLISLPMWMGLQL
ARLELELKKTPKLRKFWNLIKKNDEKMDPEAREQAYQERRFLSQLIQKFISVLKSVPLSE
PVTMDKVHYCERFIELMIDLEALLPTRRWFNTILDDSHLLVHCYLSNLVRREEDGHLFSQ
LLDMLKFYTGFEINDQTGNALTENEMTTIHYDRITSLQRAAFAHFPELYDFALSNVAEVD
TRESLVKFFGPLSSNTLHQVASYLCLLPTLPKNEDTTFDKEFLLELLVSRHERRISQIQQ
LNQMPLYPTEKIIWDENIVPTEYYSGEGCLALPKLNLQFLTLHDYLLRNFNLFRLESTYE
IRQDIEDSVSRMKPWQSEYGGVVFGGWARMAQPIVAFTVVEVAKPNIGENWPTRVRADVT
INLNVRDHIKDEWEGLRKHDVCFLITVRPTKPYGTKFDRRRPFIEQVGLVYVRGCEIQGM
LDDKGRVIEDGPEPRPNLRGESRTFRVFLDPNQYQQDMTNTIQNGAEDVYETFNIIMRRK
PKENNFKAVLETIRNLMNTDCVVPDWLHDIILGYGDPSSAHYSKMPNQIATLDFNDTFLS
IEHLKASFPGHNVKVTVEDPALQIPPFRITFPVRSGKGKKRKDADVEDEDTEEAKTLIVE
PHVIPNRGPYPYNQPKRNTIQFTHTQIEAIRAGMQPGLTMVVGPPGTGKTDVAVQIISNI
YHNFPEQRTLIVTHSNQALNQLFEKIMALDIDERHLLRLGHGEEELETEKDFSRYGRVNY
VLARRIELLEEVKRLQKSLGVPGDASYTCETAGYFFLYQVMSRWEEYISKVKNKGSTLPD
VTEVSTFFPFHEYFANAPQPIFKGRSYEEDMEIAEGCFRHIKKIFTQLEEFRASELLRSG
LDRSKYLLVKEAKIIAMTCTHAALKRHDLVKLGFKYDNILMEEAAQILEIETFIPLLLQN
PQDGFSRLKRWIMIGDHHQLPPVIKNMAFQKYSNMEQSLFTRFVRVGVPTVDLDAQGRAR
ASLCNLYNWRYKNLGNLPHVQLLPEFSTANAGLLYDFQLINVEDFQGVGESEPNPYFYQN
LGEAEYVVALFMYMCLLGYPADKISILTTYNGQKHLIRDIINRRCGNNPLIGRPNKVTTV
DRFQGQQNDYILLSLVRTRAVGHLRDVRRLVVAMSRARLGLYIFARVSLFQNCFELTPAF
SQLTARPLHLHIIPTEPFPTTRKNGERPSHEVQIIKNMPQMANFVYNMYMHLIQTTHHYH
QTLLQLPPAMVEEGEEVQNQETELETEEEAMTVQADIIPSPTDTSCRQETPAFQTDTTPS
ETGATSTPEAIPALSETTPTVVGAVSAPAEANTPQDATSAPEETK

Sequence of entity 8 (x), FASTA

>7ABI_8 Splicing factor 3B subunit 5 (chains x)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 9 (6), FASTA

>7ABI_9 U6 snRNA (chains 6)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUU

Sequence of entity 10 (B), FASTA

>7ABI_10 U2 small nuclear ribonucleoprotein B'' (chains B)
MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
NKKPGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK

Sequence of entity 11 (z), FASTA

>7ABI_11 Splicing factor 3B subunit 6 (chains z)
MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA
YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN
TDPPK

Sequence of entity 12 (q), FASTA

>7ABI_12 Ubiquitin-like protein 5 (chains q)
MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDY
EIHDGMNLELYYQ

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Townsend, C., Leelaram, M.N., Agafonov, D.E. et al. Science (2020) 370. DOI 10.1126/science.abc3753 · PubMed

Other PDB entries of the same protein (UniProt Q96DI7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
8C6J 2.8 Å, Human spliceosomal PM5 C* complex
6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
6ID0 2.9 Å, Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1…
6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
9XTT 2.92 Å, Human minor spliceosome branching-completed C complex (after step-I)
6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
8I0R 3.0 Å, The cryo-EM structure of human Bact-I complex
8I0T 3.0 Å, The cryo-EM structure of human Bact-III complex

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