7EVN: DDX42-SF3b complex

The cryo-EM structure of the DDX42-SF3b complex. Determined by electron microscopy at 2.6 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 19,668
Mol. weight: 365.73 kDa
Ligands: ZN
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7EVN contains 119 α-helices and 139 β-strands across 5 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 A: 19 helices, 112 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
β-strand	16-20	5	7
β-strand	29-33	5	7
β-strand	37-43	7	7
β-strand	50-57	8	7
β-strand	62-68	7	8
β-strand	77-82	6	8
β-strand	86-93	8	8
β-strand	98-106	9	8
β-strand	120-123	4	9
β-strand	129-133	5	9
β-strand	136	1	10
β-strand	139-143	5	9
β-strand	144-146	3	11
β-strand	152-154	3	11
β-strand	158-159	2	9
β-strand	165-173	9	10
β-strand	181-188	8	10
α-helix	204-206	3
β-strand	207-214	8	10
β-strand	219-227	9	10
β-strand	232-237	6	12
α-helix	238-239	2
β-strand	248-252	5	12
β-strand	255-259	5	12
α-helix	264-266	3
β-strand	267-270	4	12
α-helix	271-272	2
β-strand	273-274	2	13
β-strand	287-294	8	14
β-strand	299-305	7	14
β-strand	309-317	9	14
β-strand	322-332	11	14
β-strand	336-342	7	15
β-strand	346-351	6	15
β-strand	356-361	6	15
β-strand	373-374	2	14
β-strand	386-387	2	13
β-strand	395-401	7	15
α-helix	405-407	3
β-strand	409-413	5	16
β-strand	422-427	6	16
α-helix	430-432	3
β-strand	434-440	7	16
β-strand	442	1	17
β-strand	444	1	18
β-strand	448-450	3	19
β-strand	458-459	2	20
β-strand	462	1	20
β-strand	473-477	5	20
β-strand	482-486	5	20
β-strand	492	1	20
α-helix	504-505	2
β-strand	507-510	4	21
β-strand	516-520	5	21
β-strand	523-527	5	21
β-strand	534-536	3	21
α-helix	542-543	2
β-strand	544-549	6	22
β-strand	554-558	5	22
β-strand	563-564	2	22
β-strand	568	1	23
β-strand	574	1	23
β-strand	581	1	22
β-strand	587-592	6	24
α-helix	593-596	4
β-strand	604-609	6	24
β-strand	613-619	7	24
β-strand	624-632	9	24
β-strand	637-644	8	25
β-strand	663-669	7	25
β-strand	674-678	5	25
β-strand	686-689	4	25
β-strand	700	1	26
β-strand	703-706	4	27
β-strand	709-712	4	27
β-strand	715	1	26
β-strand	719	1	26
β-strand	720-724	5	27
β-strand	729-733	5	27
β-strand	734	1	17
β-strand	741	1	28
β-strand	754	1	29
β-strand	757	1	28
β-strand	762-764	3	19
β-strand	765	1	29
β-strand	767	1	18
β-strand	774-780	7	16
β-strand	785-790	6	30
β-strand	797-804	8	30
α-helix	809-824	16
α-helix	839-844	6
α-helix	849-852	4
β-strand	862-869	8	30
β-strand	876-881	6	30
β-strand	886-894	9	31
β-strand	904-911	8	31
β-strand	914-915	2	32
β-strand	918-919	2	32
β-strand	922-928	7	31
β-strand	931	1	33
β-strand	936	1	33
β-strand	939-945	7	31
β-strand	949-955	7	34
β-strand	958-963	6	34
β-strand	966-972	7	34
β-strand	977-983	7	34
β-strand	990-996	7	35
β-strand	999-1004	6	35
β-strand	1007	1	36
β-strand	1009-1015	7	35
β-strand	1020-1025	6	35
β-strand	1026	1	37
β-strand	1030	1	36
β-strand	1033-1040	8	38
β-strand	1043-1048	6	38
β-strand	1052-1057	6	38
β-strand	1088	1	37
α-helix	1089	1
β-strand	1090-1096	7	38
β-strand	1101-1108	8	6
β-strand	1115-1121	7	6
β-strand	1126-1131	6	6
α-helix	1135-1151	17
α-helix	1160-1164	5
β-strand	1171	1	38
β-strand	1173-1175	3	6
α-helix	1176-1179	4
α-helix	1180-1184	5
α-helix	1187-1196	10
α-helix	1201-1215	15

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-15	9
α-helix	28-45	18
α-helix	47-56	10
α-helix	61-70	10

Chain C: 60 helices, 0 β-strands

Element	Residues	Length
α-helix	491-497	7
α-helix	500-505	6
α-helix	509-526	18
α-helix	528-539	12
α-helix	546-562	17
α-helix	568-570	3
α-helix	571-578	8
α-helix	587-603	17
α-helix	606-613	8
α-helix	615-617	3
α-helix	622-639	18
α-helix	641-651	11
α-helix	658-675	18
α-helix	676-682	7
α-helix	683-690	8
α-helix	691-695	5
α-helix	699-716	18
α-helix	728-737	10
α-helix	741-753	13
α-helix	754-756	3
α-helix	759-777	19
α-helix	782-795	14
α-helix	803-805	3
α-helix	806-810	5
α-helix	811-818	8
α-helix	821-825	5
α-helix	828-844	17
α-helix	846-853	8
α-helix	854-857	4
α-helix	862-878	17
α-helix	889-901	13
α-helix	908-921	14
α-helix	922-924	3
α-helix	929-941	13
α-helix	946-964	19
α-helix	969-980	12
α-helix	987-1003	17
α-helix	1013-1020	8
α-helix	1021-1025	5
α-helix	1029-1045	17
α-helix	1047-1049	3
α-helix	1052-1062	11
α-helix	1063-1067	5
α-helix	1071-1088	18
α-helix	1091-1103	13
α-helix	1106-1122	17
α-helix	1125-1127	3
α-helix	1129-1136	8
α-helix	1144-1158	15
α-helix	1159-1164	6
α-helix	1166-1177	12
α-helix	1182-1198	17
α-helix	1205-1215	11
α-helix	1216-1219	4
α-helix	1224-1241	18
α-helix	1243-1250	8
α-helix	1259-1274	16
α-helix	1278-1282	5
α-helix	1284-1286	3
α-helix	1299-1301	3

Chain D: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
α-helix	13-15	3
β-strand	18-19	2	2
β-strand	21-22	2	3
β-strand	30	1	4
β-strand	39-42	4	4
β-strand	44-45	2	2
α-helix	52-54	3
β-strand	57	1	5
β-strand	58	1	3
β-strand	64	1	5
β-strand	67-68	2	3
β-strand	70-72	3	4
α-helix	73-77	5
α-helix	80-82	3
β-strand	88-90	3	1

Chain E: 32 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	71-76	6
α-helix	115-131	17
β-strand	147	1	10
α-helix	149-152	4
α-helix	156-166	11
α-helix	222-225	4
α-helix	229-238	10
β-strand	241-244	4	39
α-helix	248-251	4
α-helix	255-258	4
α-helix	262-270	9
α-helix	278-288	11
β-strand	293-296	4	39
α-helix	303-316	14
α-helix	319-322	4
β-strand	329-332	4	39
α-helix	336-350	15
α-helix	351-353	3
β-strand	357-360	4	39
α-helix	366-375	10
β-strand	379-382	4	39
α-helix	384-392	9
β-strand	403-406	4	39
α-helix	409-414	6
α-helix	418-427	10
β-strand	433-438	6	39
α-helix	443-452	10
α-helix	456	1
β-strand	457-461	5	39
α-helix	462-464	3
β-strand	472-477	6	40
α-helix	481-483	3
α-helix	484-496	13
β-strand	500-505	6	40
α-helix	508-520	13
β-strand	525-528	4	40
α-helix	534-545	12
β-strand	551-555	5	40
α-helix	556-558	3
β-strand	567-572	6	40
α-helix	575-576	2
α-helix	579-586	8
β-strand	597-602	6	40
α-helix	604-606	3
α-helix	607-619	13
α-helix	626-632	7
α-helix	636-639	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Splicing factor 3B subunit 5	B	protein	86	Homo sapiens	Q9BWJ5 (AlphaFold model)
Splicing factor 3B subunit 1	C	protein	872	Homo sapiens	O75533 (AlphaFold model)
PHD finger-like domain-containing protein 5A	D	protein	110	Homo sapiens	Q7RTV0 (AlphaFold model)
Splicing factor 3B subunit 3	A	protein	1250	Homo sapiens	Q15393 (AlphaFold model)
ATP-dependent RNA helicase DDX42	E	protein	958	Homo sapiens	Q86XP3

Sequence of entity 1 (B), FASTA

>7EVN_1 Splicing factor 3B subunit 5 (chains B)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 2 (C), FASTA

>7EVN_2 Splicing factor 3B subunit 1 (chains C)
MASDYKDDDDKASDEVDAGTMKSVNDQPSGNLPFLKPDDIQYFDKLLVDVDESTLSPEEQ
KERKIMKLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLMSPTLEDQERHLL
VKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAAGLATMIST
MRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIA
ILMGCAILPHLRSLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYGIESFDSVLKPLW
KGIRQHRGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSPDEEMKKIVLKVV
KQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVELANKVGAAEIISR
IVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAFQEQTTEDSVMLN
GFGTVVNALGKRVKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMG
HLGVVLYEYLGEEYPEVLGSILGALKAIVNVIGMHKMTPPIKDLLPRLTPILKNRHEKVQ
ENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYIAKAIGPHD
VLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLS
FLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVYGFGCEDSLNHLL
NYVWPNVFETSPHVIQAVMGALEGLRVAIGPCRMLQYCLQGLFHPARKVRDVYWKIYNSI
YIGSQDALIAHYPRIYNDDKNTYIRYELDYIL

Sequence of entity 3 (D), FASTA

>7EVN_3 PHD finger-like domain-containing protein 5A (chains D)
MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI
CGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR

Sequence of entity 4 (A), FASTA

>7EVN_4 Splicing factor 3B subunit 3 (chains A)
WSHPQFEKGGGSGGGSGGSAWSHPQFEKGSAAAMFLYNLTLQRATGISFAIHGNFSGTKQ
QEIVVSRGKILELLRPDPNTGKVHTLLTVEVFGVIRSLMAFRLTGGTKDYIVVGSDSGRI
VILEYQPSKNMFEKIHQETFGKSGCRRIVPGQFLAVDPKGRAVMISAIEKQKLVYILNRD
AAARLTISSPLEAHKANTLVYHVVGVDVGFENPMFACLEMDYEEADNDPTGEAAANTQQT
LTFYELDLGLNHVVRKYSEPLEEHGNFLITVPGGSDGPSGVLICSENYITYKNFGDQPDI
RCPIPRRRNDLDDPERGMIFVCSATHKTKSMFFFLAQTEQGDIFKITLETDEDMVTEIRL
KYFDTVPVAAAMCVLKTGFLFVASEFGNHYLYQIAHLGDDDEEPEFSSAMPLEEGDTFFF
QPRPLKNLVLVDELDSLSPILFCQIADLANEDTPQLYVACGRGPRSSLRVLRHGLEVSEM
AVSELPGNPNAVWTVRRHIEDEFDAYIIVSFVNATLVLSIGETVEEVTDSGFLGTTPTLS
CSLLGDDALVQVYPDGIRHIRADKRVNEWKTPGKKTIVKCAVNQRQVVIALTGGELVYFE
MDPSGQLNEYTERKEMSADVVCMSLANVPPGEQRSRFLAVGLVDNTVRIISLDPSDCLQP
LSMQALPAQPESLCIVEMGGTEKQDELGERGSIGFLYLNIGLQNGVLLRTVLDPVTGDLS
DTRTRYLGSRPVKLFRVRMQGQEAVLAMSSRSWLSYSYQSRFHLTPLSYETLEFASGFAS
EQCPEGIVAISTNTLRILALEKLGAVFNQVAFPLQYTPRKFVIHPESNNLIIIETDHNAY
TEATKAQRKQQMAEEMVEAAGEDERELAAEMAAAFLNENLPESIFGAPKAGNGQWASVIR
VMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTGEDWYVLVGVAKDLILNPRSVAGGFVYT
YKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVLIGVGKLLRVYDLGKKKLLRKCENKHIA
NYISGIQTIGHRVIVSDVQESFIWVRYKRNENQLIIFADDTYPRWVTTASLLDYDTVAGA
DKFGNICVVRLPPNTNDEVDEDPTGNKALWDRGLLNGASQKAEVIMNYHVGETVLSLQKT
TLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLRSEHPPLCGRDHLSFRSYY
FPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRTPPEVSKKLEDIRTRYAF

Sequence of entity 5 (E), FASTA

>7EVN_5 ATP-dependent RNA helicase DDX42 (chains E)
MASDYKDDDDKASDEVDAGTMNWNKGGPGTKRGFGFGGFAISAGKKEEPKLPQQSHSAFG
ATSSSSGFGKSAPPQLPSFYKIGSKRANFDEENAYFEDEEEDSSNVDLPYIPAENSPTRQ
QFHSKPVDSDSDDDPLEAFMAEVEDQAARDMKRLEEKDKERKNVKGIRDDIEEEDDQEAY
FRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKKIIDPLPPIDHSEIDYPPFEKNFYNE
HEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMHQIRKSEYTQPTPIQ
CQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDGPIAVIVCPTRELCQ
QIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRLIDHVKKKATNLQR
VSYLVFDEADRMFDMGFEYQVRSIASHVRPDRQTLLFSATFRKKIEKLARDILIDPIRVV
QGDIGEANEDVTQIVEILHSGPSKWNWLTRRLVEFTSSGSVLLFVTKKANAEELANNLKQ
EGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARGLDIPSIKTVINYDVARDID
THTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDLVRNLEGANQHVSKELLDLAMQNAWFRK
SRFKGGKGKKLNIGGGGLGYRERPGLGSENMDRGNNNVMSNYEAYKPSTGAMGDRLTAMK
AAFQSQYKSHFVAASLSNQKAGSSAAGASGWTSAGSLNSVPTNSAQQGHNSPDSPVTSAA
KGIPGFGNTGNISGAPVTYPSAGAQGVNNTASGNNSREGTGGSNGKRERYTENRGSSRHS
HGETGNRHSDSPRHGDGGRHGDGYRHPESSSRHTDGHRHGENRHGGSAGRHGENRGANDG
RNGESRKEAFNRESKMEPKMEPKVDSSKMDKVDSKTDKTADGFAVPEPPKRKKSRWDS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Structural insights into branch site proofreading by human spliceosome. Zhang, X., Zhan, X., Bian, T. et al. Nat Struct Mol Biol (2024). DOI 10.1038/s41594-023-01188-0

Other PDB entries of the same protein (UniProt Q9BWJ5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q4O 2.1 Å, Substrate-bound A-like U2 snRNP
7Q4P 2.15 Å, U2 snRNP after ATP-dependent remodelling
7Q3L 2.21 Å, Human 17S U2 snRNP 5' domain
7B9C 2.4 Å, Structure of a minimal SF3B core in complex with spliceostatin A (form I)
9RDK 2.41 Å, Cryo-EM structure of the human SAGA co-activator complex
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
7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
7B0I 3.0 Å, Structure of a minimal SF3B core in complex with spliceostatin A (form II)
7B91 3.0 Å, Structure of a minimal SF3B core in complex with pladienolide D (form I)

Browse structure collections

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