7Q4O: Substrate-bound A-like U2 snRNP

Substrate-bound A-like U2 snRNP. Determined by electron microscopy at 2.1 Å resolution. Released 30 Mar 2022.

Method: Electron microscopy
Resolution: 2.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 10
Atoms: 21,212
Mol. weight: 593.52 kDa
Ligands: ZN
Released: 30 Mar 2022

Explore 7Q4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q4O contains 124 α-helices and 131 β-strands across 8 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: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	46-48	3	1
β-strand	54-56	3	1
β-strand	61-63	3	1
α-helix	66-73	8
α-helix	76-82	7

Chain 9: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	396-399	4
β-strand	407-408	2	2
β-strand	414-415	2	2
α-helix	419-425	7
α-helix	429-438	10
α-helix	444-446	3
α-helix	452-469	18
α-helix	473-476	4
β-strand	479-480	2	3
β-strand	486-487	2	3

Chain A: 63 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	401-405	5
β-strand	412-414	3	4
α-helix	492-505	14
α-helix	509-526	18
α-helix	528-539	12
α-helix	546-563	18
α-helix	564-570	7
α-helix	571-578	8
α-helix	579-582	4
α-helix	587-603	17
α-helix	606-613	8
α-helix	616-618	3
α-helix	622-636	15
α-helix	641-651	11
α-helix	658-675	18
α-helix	676-682	7
α-helix	683-690	8
α-helix	691-694	4
α-helix	699-716	18
α-helix	721-723	3
α-helix	725-737	13
α-helix	740-753	14
α-helix	754-756	3
α-helix	759-776	18
α-helix	782-797	16
α-helix	803-805	3
α-helix	806-810	5
α-helix	811-818	8
α-helix	821-825	5
α-helix	827-844	18
α-helix	846-853	8
α-helix	854-858	5
α-helix	862-879	18
α-helix	886-901	16
α-helix	908-921	14
α-helix	922-925	4
α-helix	929-940	12
α-helix	945-958	14
α-helix	961-963	3
α-helix	967-980	14
α-helix	981-983	3
α-helix	987-1003	17
α-helix	1013-1025	13
α-helix	1029-1045	17
α-helix	1047-1049	3
α-helix	1052-1065	14
α-helix	1071-1088	18
α-helix	1090-1099	10
α-helix	1100-1102	3
α-helix	1106-1122	17
α-helix	1125-1137	13
α-helix	1141-1158	18
α-helix	1159-1161	3
α-helix	1162-1177	16
α-helix	1182-1198	17
α-helix	1205-1215	11
α-helix	1216-1220	5
α-helix	1224-1241	18
α-helix	1243-1250	8
α-helix	1251-1253	3
α-helix	1259-1283	25
α-helix	1284-1286	3
α-helix	1288-1290	3
α-helix	1299-1301	3

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	459-461	3
α-helix	462-468	7
α-helix	472-474	3
α-helix	479-481	3
α-helix	485-492	8
α-helix	497-501	5
α-helix	502-505	4
α-helix	509	1
α-helix	520-522	3
α-helix	526-529	4
α-helix	533-536	4
α-helix	568-576	9
α-helix	584-586	3
α-helix	706-707	2
α-helix	710-713	4

Chain C: 26 helices, 104 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
β-strand	16-20	5	6
β-strand	29-33	5	6
β-strand	37-44	8	6
β-strand	49-57	9	6
β-strand	62-68	7	7
α-helix	76	1
β-strand	77-82	6	7
β-strand	86-93	8	7
β-strand	98-106	9	7
β-strand	120-123	4	8
β-strand	129-133	5	8
β-strand	136	1	9
β-strand	139-143	5	8
β-strand	144-146	3	10
β-strand	152-154	3	10
α-helix	155-157	3
β-strand	158-159	2	8
β-strand	165-173	9	9
α-helix	180	1
β-strand	181-188	8	9
α-helix	191-193	3
α-helix	199-203	5
α-helix	204-206	3
β-strand	207-214	8	9
β-strand	219-227	9	9
β-strand	232-237	6	11
α-helix	238-239	2
β-strand	248-252	5	11
β-strand	255-259	5	11
α-helix	264-266	3
β-strand	267-270	4	11
α-helix	271-272	2
β-strand	273-274	2	12
β-strand	287-294	8	13
β-strand	299-305	7	13
β-strand	309-318	10	13
β-strand	321-332	12	13
β-strand	336-342	7	14
β-strand	346-351	6	14
β-strand	356-361	6	14
α-helix	370-371	2
β-strand	372-374	3	13
β-strand	386-387	2	12
β-strand	395-401	7	14
α-helix	405	1
α-helix	407	1
β-strand	409-413	5	15
β-strand	422-427	6	15
α-helix	430-432	3
β-strand	434-440	7	15
β-strand	442	1	16
β-strand	444-451	8	17
β-strand	456-462	7	18
β-strand	473-478	6	18
β-strand	481-485	5	18
β-strand	493	1	18
β-strand	507-512	6	19
β-strand	515-520	6	19
β-strand	523-528	6	19
β-strand	533-537	5	19
β-strand	544-550	7	20
β-strand	553-558	6	20
β-strand	562-569	8	20
β-strand	573-576	4	20
β-strand	581-582	2	20
β-strand	587-592	6	21
α-helix	593-596	4
β-strand	604-609	6	21
β-strand	613-618	6	21
β-strand	627-632	6	21
β-strand	637-644	8	22
β-strand	663-669	7	22
β-strand	673-678	6	22
β-strand	686-690	5	22
β-strand	701-706	6	23
β-strand	709-714	6	23
β-strand	720-725	6	23
β-strand	728-733	6	23
β-strand	734	1	16
β-strand	741-745	5	17
β-strand	753-758	6	17
β-strand	761-767	7	17
β-strand	774-780	7	15
β-strand	785-790	6	24
β-strand	797-804	8	24
β-strand	806	1	25
α-helix	809-825	17
α-helix	831-844	14
α-helix	849-852	4
β-strand	856	1	25
β-strand	862-869	8	24
β-strand	876-881	6	24
α-helix	882-883	2
β-strand	886-894	9	26
β-strand	903-911	9	26
β-strand	914	1	27
β-strand	919	1	27
β-strand	923-931	9	26
β-strand	936-945	10	26
β-strand	949-955	7	28
β-strand	958-963	6	28
β-strand	966-971	6	28
β-strand	978-983	6	28
β-strand	990-996	7	29
β-strand	999-1004	6	29
β-strand	1007	1	30
β-strand	1009-1015	7	29
β-strand	1020-1026	7	29
β-strand	1031	1	30
β-strand	1033-1040	8	31
β-strand	1043-1048	6	31
β-strand	1052-1057	6	31
α-helix	1058-1059	2
β-strand	1081	1	32
β-strand	1084	1	32
β-strand	1088	1	29
β-strand	1090-1096	7	31
β-strand	1101-1107	7	5
α-helix	1113-1115	3
β-strand	1116-1121	6	5
β-strand	1126-1131	6	5
α-helix	1135-1151	17
α-helix	1160-1164	5
β-strand	1171	1	31
β-strand	1173-1175	3	5
α-helix	1176-1179	4
α-helix	1180-1184	5
α-helix	1187-1196	10
α-helix	1201-1214	14

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	33
β-strand	21	1	33
α-helix	28-45	18
α-helix	47-57	11
α-helix	61-71	11

Chain F: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	4
α-helix	32-40	9
β-strand	45-51	7	4
β-strand	60-64	5	4
α-helix	67-77	11
β-strand	81-82	2	34
β-strand	85-86	2	34
β-strand	88-91	4	4
α-helix	94-97	4

Chain G: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	35
β-strand	18-19	2	36
α-helix	20	1
β-strand	21-22	2	37
β-strand	39-42	4	38
α-helix	43	1
β-strand	44-45	2	36
α-helix	47-50	4
α-helix	52-54	3
β-strand	57	1	39
β-strand	58	1	37
β-strand	64	1	39
β-strand	67-68	2	37
β-strand	70-72	3	38
α-helix	73-77	5
α-helix	80-82	3
β-strand	88	1	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Splicing factor 3A subunit 2	1	protein	464	Homo sapiens	Q15428 (AlphaFold model)
U2 snRNA	2	RNA	188	Homo sapiens
Splicing factor 3A subunit 3	9	protein	501	Homo sapiens	Q12874 (AlphaFold model)
Splicing factor 3B subunit 1	A	protein	1304	Homo sapiens	O75533 (AlphaFold model)
Splicing factor 3B subunit 2	B	protein	895	Homo sapiens	Q13435 (AlphaFold model)
Splicing factor 3B subunit 3	C	protein	1217	Homo sapiens	Q15393
Splicing factor 3B subunit 5	E	protein	86	Homo sapiens	Q9BWJ5
Splicing factor 3B subunit 6	F	protein	125	Homo sapiens	Q9Y3B4
PHD finger-like domain-containing protein 5A	G	protein	110	Homo sapiens	Q7RTV0
BPS oligo	h	RNA	17	synthetic construct

Sequence of entity 1 (1), FASTA

>7Q4O_1 Splicing factor 3A subunit 2 (chains 1)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN

Sequence of entity 2 (2), FASTA

>7Q4O_2 U2 snRNA (chains 2)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC

Sequence of entity 3 (9), FASTA

>7Q4O_3 Splicing factor 3A subunit 3 (chains 9)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL

Sequence of entity 4 (A), FASTA

>7Q4O_4 Splicing factor 3B subunit 1 (chains A)
MAKIAKTHEDIEAQIREIQGKKAALDEAQGVGLDSTGYYDQEIYGGSDSRFAGYVTSIAA
TELEDDDDDYSSSTSLLGQKKPGYHAPVALLNDIPQSTEQYDPFAEHRPPKIADREDEYK
KHRRTMIISPERLDPFADGGKTPDPKMNARTYMDVMREQHLTKEEREIRQQLAEKAKAGE
LKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAETPGHTPSLRWDETPGRAK
GSETPGATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRWDETPKTE
RDTPGHGSGWAETPRTDRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPI
GTPAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKVLPPPAG
YVPIRTPARKLTATPTPLGGMTGFHMQTEDRTMKSVNDQPSGNLPFLKPDDIQYFDKLLV
DVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLM
SPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNL
AKAAGLATMISTMRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQA
RHTGIKIVQQIAILMGCAILPHLRSLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYG
IESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSP
DEEMKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVEL
ANKVGAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAF
QEQTTEDSVMLNGFGTVVNALGKRVKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAV
VMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVIGMHKMTPPIKDLLPRL
TPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNT
FGYIAKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPE
LNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVY
GFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPCRMLQYCLQGLFHPARK
VRDVYWKIYNSIYIGSQDALIAHYPRIYNDDKNTYIRYELDYIL

Sequence of entity 5 (B), FASTA

>7Q4O_5 Splicing factor 3B subunit 2 (chains B)
MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF

Sequence of entity 6 (C), FASTA

>7Q4O_6 Splicing factor 3B subunit 3 (chains C)
MFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEVFG
VIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPGQF
LAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFENP
MFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITVPG
GSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSMFF
FLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQ
IAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANEDT
PQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVN
ATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKTPG
KKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPGEQ
RSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERGSI
GFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSW
LSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVAFP
LQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAA
AFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTG
EDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVL
IGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQ
LIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDEDPTGNKALWDRG
LLNGASQKAEVIMNYHVGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDF
FQHVEMHLRSEHPPLCGRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRT
PPEVSKKLEDIRTRYAF

Sequence of entity 7 (E), FASTA

>7Q4O_7 Splicing factor 3B subunit 5 (chains E)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 8 (F), FASTA

>7Q4O_8 Splicing factor 3B subunit 6 (chains F)
MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA
YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN
TDPPK

Sequence of entity 9 (G), FASTA

>7Q4O_9 PHD finger-like domain-containing protein 5A (chains G)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR

Sequence of entity 10 (h), FASTA

>7Q4O_10 BPS oligo (chains h)
CAGAUACUAACACUUGA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5

Primary citation

Structural basis of branch site recognition by the human spliceosome. Tholen, J., Razew, M., Weis, F. et al. Science (2022) 375:50-57. DOI 10.1126/science.abm4245 · PubMed

Other PDB entries of the same protein (UniProt Q15428 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q4P 2.15 Å, U2 snRNP after ATP-dependent remodelling
7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
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.
8HK1 2.7 Å, The cryo-EM structure of human pre-17S U2 snRNP
7VPX 3.0 Å, The cryo-EM structure of the human pre-A complex
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
7ONB 3.1 Å, Structure of the U2 5' module of the A3'-SSA complex
7QTT 3.1 Å, Structural organization of a late activated human spliceosome (Baqr, core region)
8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.
8H6J 3.25 Å, Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state.

Browse structure collections

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