7Q4P: U2 snRNP after ATP-dependent remodelling

U2 snRNP after ATP-dependent remodelling. Determined by electron microscopy at 2.15 Å resolution. Released 30 Mar 2022.

Method: Electron microscopy
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,451
Mol. weight: 573.56 kDa
Ligands: ZN
Released: 30 Mar 2022

Explore 7Q4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q4P contains 70 α-helices and 92 β-strands across 7 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	66-74	9
α-helix	76-80	5

Chain 9: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	394-399	6
β-strand	405-408	4	2
β-strand	414-417	4	2
α-helix	419-425	7
α-helix	429-438	10
α-helix	444-446	3
α-helix	452-467	16
β-strand	479-480	2	3
β-strand	486-487	2	3

Chain A: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	1052-1062	11
α-helix	1065-1067	3
α-helix	1071-1087	17
α-helix	1090-1098	9
α-helix	1099-1101	3
α-helix	1106-1122	17
α-helix	1125-1134	10
α-helix	1141-1158	18
α-helix	1159-1165	7
α-helix	1166-1177	12
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	1259-1276	18
α-helix	1280-1283	4
α-helix	1284-1286	3
α-helix	1298-1301	4

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	459-461	3
α-helix	462-468	7
α-helix	478-481	4
α-helix	485-493	9
α-helix	499-501	3
α-helix	502-504	3
α-helix	519-525	7
α-helix	526-529	4
α-helix	569-576	8
α-helix	706-707	2

Chain C: 23 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	4
β-strand	16-20	5	5
β-strand	29-33	5	5
β-strand	37-43	7	5
β-strand	50-57	8	5
β-strand	62-68	7	6
β-strand	77-82	6	6
β-strand	86-93	8	6
β-strand	98-106	9	6
β-strand	120-123	4	7
β-strand	129-133	5	7
β-strand	136	1	8
β-strand	139-143	5	7
β-strand	144-146	3	9
β-strand	152-154	3	9
α-helix	155-157	3
β-strand	158-159	2	7
β-strand	165-173	9	8
α-helix	180	1
β-strand	181-188	8	8
α-helix	199-202	4
α-helix	204-206	3
β-strand	207-214	8	8
β-strand	219-227	9	8
β-strand	232-237	6	10
β-strand	248-252	5	10
β-strand	255-259	5	10
α-helix	264-266	3
β-strand	267-270	4	10
α-helix	271-272	2
β-strand	273-274	2	11
β-strand	287-294	8	12
β-strand	299-305	7	12
β-strand	309-318	10	12
β-strand	321-332	12	12
α-helix	334-335	2
β-strand	336-342	7	13
β-strand	346-351	6	13
β-strand	356-361	6	13
β-strand	372-374	3	12
β-strand	386-387	2	11
β-strand	395-401	7	13
α-helix	405	1
β-strand	407-413	7	14
α-helix	421	1
β-strand	422-427	6	14
α-helix	430-432	3
β-strand	434-440	7	14
β-strand	774-780	7	14
β-strand	785-790	6	15
β-strand	797-804	8	15
β-strand	806	1	16
α-helix	809-825	17
α-helix	834-844	11
α-helix	849-852	4
β-strand	856	1	16
β-strand	862-869	8	15
β-strand	876-881	6	15
α-helix	882-883	2
β-strand	886-895	10	17
β-strand	903-911	9	17
β-strand	914-915	2	18
β-strand	918-919	2	18
β-strand	923-931	9	17
β-strand	936-945	10	17
β-strand	949-955	7	19
β-strand	958-963	6	19
β-strand	966-971	6	19
α-helix	977	1
β-strand	978-983	6	19
β-strand	990-996	7	20
β-strand	999-1004	6	20
β-strand	1007	1	21
β-strand	1009-1015	7	20
β-strand	1020-1026	7	20
β-strand	1031	1	21
β-strand	1033-1038	6	22
β-strand	1043-1048	6	22
β-strand	1052-1057	6	22
α-helix	1058-1059	2
α-helix	1074-1077	4
β-strand	1081	1	23
β-strand	1084	1	23
β-strand	1087-1088	2	20
β-strand	1090-1096	7	22
β-strand	1101-1107	7	4
β-strand	1116-1121	6	4
β-strand	1126-1131	6	4
α-helix	1135-1151	17
α-helix	1160-1164	5
β-strand	1171	1	22
β-strand	1173-1175	3	4
α-helix	1176-1179	4
α-helix	1182-1184	3
α-helix	1187-1196	10
α-helix	1201-1215	15

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	28-45	18
α-helix	47-57	11
α-helix	61-71	11

Chain G: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	24
α-helix	14-15	2
β-strand	18-19	2	25
α-helix	20	1
β-strand	21-22	2	26
β-strand	30	1	27
β-strand	39-42	4	27
α-helix	43	1
β-strand	44-45	2	25
α-helix	47-49	3
α-helix	52-54	3
β-strand	57	1	28
β-strand	58	1	26
β-strand	64	1	28
β-strand	67-68	2	26
β-strand	70-72	3	27
α-helix	73-77	5
α-helix	80-82	3
β-strand	88	1	24

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
PHD finger-like domain-containing protein 5A	G	protein	110	Homo sapiens	Q7RTV0

Sequence of entity 1 (1), FASTA

>7Q4P_1 Splicing factor 3A subunit 2 (chains 1)
MDFQHRPGGKTGSGGVASSSESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCL
TLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVT
KQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIA
FKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPPPLMNG
LPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLPPPAPGVHPPAPVVHPPASG
VHPPAPGVHPPAPGVHPPAPGVHPPTSGVHPPAPGVHPPAPGVHPPAPGVHPPAPGVHPP
APGVHPPPSAGVHPQAPGVHPAAPAVHPQAPGVHPPAPGMHPQAPGVHPQPPGVHPSAPG
VHPQPPGVHPSNPGVHPPTPMPPMLRPPLPSEGPGNIPPPPPTN

Sequence of entity 2 (2), FASTA

>7Q4P_2 U2 snRNA (chains 2)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAUGGAUUUUUGGAGCAGGGAGAUGGA
AUAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACG
GUGCACCC

Sequence of entity 3 (9), FASTA

>7Q4P_3 Splicing factor 3A subunit 3 (chains 9)
METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDL
YDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENP
SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNA
EYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQAEFEKKWENGTFPGWPKETSSALTHA
GAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTKGKSLESLDTSL
FAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEE
EEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYE
DSSGNVVNKKTYEDLKRQGLL

Sequence of entity 4 (A), FASTA

>7Q4P_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

>7Q4P_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

>7Q4P_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

>7Q4P_7 Splicing factor 3B subunit 5 (chains E)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 8 (G), FASTA

>7Q4P_8 PHD finger-like domain-containing protein 5A (chains G)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR

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:

7Q4O 2.1 Å, Substrate-bound A-like U2 snRNP
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.

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