7OMF: Minimal SF3B core

Structure of a minimal SF3B core in complex with sudemycin D6 (form I). Determined by X-ray diffraction at 3.0 Å resolution. Released 4 Aug 2021.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,852
Mol. weight: 219.89 kDa
Ligands: ZN, T2W, SCN
Released: 4 Aug 2021

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

Secondary structure: helices and β-sheets

7OMF contains 91 α-helices and 80 β-strands across 4 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: 18 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	-1-2	4
β-strand	3-9	7	1
β-strand	16-20	5	2
β-strand	29-33	5	2
β-strand	37-44	8	2
β-strand	49-57	9	2
β-strand	64-68	5	3
β-strand	77-81	5	3
β-strand	86-93	8	3
β-strand	98-106	9	3
β-strand	120-123	4	4
β-strand	129-133	5	4
β-strand	136	1	5
β-strand	139-143	5	4
β-strand	144-146	3	6
β-strand	152-154	3	6
β-strand	158-159	2	4
β-strand	165-173	9	5
β-strand	181-188	8	5
α-helix	190-193	4
α-helix	199-203	5
β-strand	207-214	8	5
β-strand	219-227	9	5
β-strand	232-237	6	7
α-helix	238-239	2
β-strand	248-252	5	7
β-strand	255-259	5	7
α-helix	264-266	3
β-strand	267-270	4	7
α-helix	271-272	2
β-strand	273-274	2	8
β-strand	287-294	8	9
β-strand	299-305	7	9
β-strand	309-318	10	9
β-strand	321-332	12	9
β-strand	336-342	7	10
β-strand	346-351	6	10
β-strand	356-361	6	10
α-helix	371	1
β-strand	372-374	3	9
β-strand	386-387	2	8
β-strand	395-401	7	10
α-helix	405	1
β-strand	407-413	7	11
β-strand	422-427	6	11
α-helix	430-432	3
β-strand	434-439	6	11
β-strand	775-780	6	11
β-strand	785-790	6	12
β-strand	797-804	8	12
α-helix	809-824	16
α-helix	832-844	13
α-helix	849-852	4
β-strand	862-869	8	12
β-strand	876-881	6	12
β-strand	886-895	10	13
β-strand	903-911	9	13
β-strand	914	1	14
β-strand	919	1	14
β-strand	922-928	7	13
β-strand	939-945	7	13
β-strand	949-955	7	15
β-strand	958-963	6	15
β-strand	966-972	7	15
β-strand	977-983	7	15
β-strand	990-996	7	16
β-strand	999-1004	6	16
β-strand	1007	1	17
β-strand	1009-1015	7	16
β-strand	1020-1026	7	16
β-strand	1031	1	17
β-strand	1033-1038	6	18
β-strand	1043-1048	6	18
β-strand	1052-1057	6	18
β-strand	1070	1	16
β-strand	1072-1078	7	18
β-strand	1083-1089	7	1
β-strand	1098-1103	6	1
β-strand	1108-1113	6	1
α-helix	1117-1133	17
α-helix	1142-1146	5
β-strand	1153	1	18
β-strand	1155-1157	3	1
α-helix	1158-1161	4
α-helix	1162-1166	5
α-helix	1169-1178	10
α-helix	1183-1196	14

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	28-45	18
α-helix	47-56	10
α-helix	61-71	11

Chain C: 62 helices, 0 β-strands

Element	Residues	Length
α-helix	469-475	7
α-helix	476-478	3
α-helix	489-505	17
α-helix	509-521	13
α-helix	523-526	4
α-helix	529-539	11
α-helix	546-560	15
α-helix	571-578	8
α-helix	579-583	5
α-helix	587-604	18
α-helix	606-613	8
α-helix	615-618	4
α-helix	622-639	18
α-helix	641-652	12
α-helix	658-675	18
α-helix	676-679	4
α-helix	683-690	8
α-helix	691-695	5
α-helix	699-716	18
α-helix	721-727	7
α-helix	728-737	10
α-helix	741-753	13
α-helix	754-756	3
α-helix	759-775	17
α-helix	776-778	3
α-helix	782-795	14
α-helix	803-805	3
α-helix	806-810	5
α-helix	811-817	7
α-helix	821-825	5
α-helix	827-844	18
α-helix	846-850	5
α-helix	855-857	3
α-helix	862-879	18
α-helix	886-901	16
α-helix	908-921	14
α-helix	922-928	7
α-helix	929-940	12
α-helix	945-964	20
α-helix	968-980	13
α-helix	987-1001	15
α-helix	1013-1020	8
α-helix	1021-1025	5
α-helix	1029-1045	17
α-helix	1047-1049	3
α-helix	1052-1065	14
α-helix	1071-1088	18
α-helix	1090-1103	14
α-helix	1107-1122	16
α-helix	1125-1136	12
α-helix	1141-1158	18
α-helix	1159-1164	6
α-helix	1166-1176	11
α-helix	1182-1198	17
α-helix	1205-1215	11
α-helix	1216-1219	4
α-helix	1224-1241	18
α-helix	1243-1254	12
α-helix	1259-1275	17
α-helix	1279-1282	4
α-helix	1284-1286	3
α-helix	1298-1301	4

Chain D: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	19
α-helix	14-15	2
β-strand	18-19	2	20
α-helix	20	1
β-strand	21-22	2	21
β-strand	39-42	4	22
α-helix	43	1
β-strand	44-45	2	20
α-helix	52-54	3
β-strand	57	1	23
β-strand	58	1	21
α-helix	63	1
β-strand	64	1	23
α-helix	65	1
β-strand	67-68	2	21
β-strand	70-72	3	22
α-helix	73-77	5
α-helix	80-82	3
β-strand	88-90	3	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Splicing factor 3B subunit 3	A	protein	899	Homo sapiens	Q15393 (AlphaFold model)
Splicing factor 3B subunit 5	B	protein	86	Homo sapiens	Q9BWJ5 (AlphaFold model)
Splicing factor 3B subunit 1	C	protein	852	Homo sapiens	O75533 (AlphaFold model)
PHD finger-like domain-containing protein 5A	D	protein	108	Homo sapiens	Q7RTV0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7OMF_1 Splicing factor 3B subunit 3 (chains A)
GAEFKGLRRHMFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKV
HTLLTVEVFGVIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKS
GCRRIVPGQFLAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHV
VGVDVGFENPMFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEE
HGNFLITVPGGSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCS
ATHKTKSMFFFLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVA
SEFGNHYLYQIAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFC
QIADLANEDTPQLYVACGRGPRSSLRVLRHGLGGNGNSGEKLGAVFNQVAFPLQYTPRKF
VIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEMAAAFLNENLP
ESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSNTGEDWYVLVG
VAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGRVLIGVGKLLR
VYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNENQLIIFADDT
YPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDSQKAEVIMNYHVGETVLSLQK
TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLRSEHPPLCGRDHLSFRSY
YFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRTPPEVSKKLEDIRTRYAFDYKDDDDK

Sequence of entity 2 (B), FASTA

>7OMF_2 Splicing factor 3B subunit 5 (chains B)
MTDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENES
KARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 3 (C), FASTA

>7OMF_3 Splicing factor 3B subunit 1 (chains C)
MKSVNDQPSGNLPFLKPDDIQYFDKLLVDVDESTLSPEEQKERKIMKLLLKIKNGTPPMR
KAALRQITDKAREFGAGPLFNQILPLLMSPTLEDQERHLLVKVIDRILYKLDDLVRPYVH
KILVVIEPLLIDEDYYARVEGREIISNLAKAAGLATMISTMRPDIDNMDEYVRNTTARAF
AVVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHLRSLVEIIEH
GLVDEQQKVRTISALAIAALAEAATPYGIESFDSVLKPLWKGIRQHRGKGLAAFLKAIGY
LIPLMDAEYANYYTREVMLILIREFQSPDEEMKKIVLKVVKQCCGTDGVEANYIKTEILP
PFFKHFWQHRMALDRRNYRQLVDTTVELANKVGAAEIISRIVDDLKDEAEQYRKMVMETI
EKIMGNLGAADIDHKLEEQLIDGILYAFQEQTTEDSVMLNGFGTVVNALGKRVKPYLPQI
CGTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGS
ILGALKAIVNVIGMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRIADRGAEYVSA
REWMRICFELLELLKAHKKAIRRATVNTFGYIAKAIGPHDVLATLLNNLKVQERQNRVCT
TVAIAIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYIGEMGKDYIYAVTPL
LEDALMDRDLVHRQTASAVVQHMSLGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMG
ALEGLRVAIGPCRMLQYCLQGLFHPARKVRDVYWKIYNSIYIGSQDALIAHYPRIYNDDK
NTYIRYELDYIL

Sequence of entity 4 (D), FASTA

>7OMF_4 PHD finger-like domain-containing protein 5A (chains D)
GPLGSPGSRAMAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECN
YGSYQGRCVICGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
T2W	[(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S},4~{R})-4,6,6-trimethyl-4-…	C27 H44 N2 O5	1
SCN	Thiocyanate ion	C N S	1

Primary citation

Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Cretu, C., Gee, P., Liu, X. et al. Nat Commun (2021) 12:4491-4491. DOI 10.1038/s41467-021-24741-1 · PubMed

Other PDB entries of the same protein (UniProt Q15393 (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
7EVN 2.6 Å, The cryo-EM structure of the DDX42-SF3b complex
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)

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