6EN4: SF3b core

Name: PDB 6EN4: SF3b core in complex with a splicing modulator
Published: 2018-06-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: splicing

SF3b core in complex with a splicing modulator. Determined by X-ray diffraction at 3.08 Å resolution. Released 20 Jun 2018.

Method: X-ray diffraction
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 4
Atoms: 17,246
Mol. weight: 254.06 kDa
Ligands: BGZ, ZN
Released: 20 Jun 2018

Explore 6EN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EN4 contains 91 α-helices and 114 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: 19 helices, 103 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
β-strand	16-20	5	2
β-strand	29-33	5	2
β-strand	37-43	7	2
β-strand	50-57	8	2
β-strand	62-68	7	3
β-strand	77-82	6	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
α-helix	156-157	2
β-strand	158-159	2	4
β-strand	165-173	9	5
β-strand	181-188	8	5
β-strand	207-214	8	5
β-strand	219-227	9	5
β-strand	232-238	7	7
α-helix	239	1
β-strand	247-252	6	7
β-strand	255-258	4	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	309-313	5	9
β-strand	314-318	5	10
β-strand	321-328	8	10
β-strand	329-332	4	9
α-helix	335	1
β-strand	336-342	7	11
β-strand	346-351	6	11
β-strand	356-361	6	11
β-strand	372-374	3	10
β-strand	386-387	2	8
β-strand	395-401	7	11
β-strand	407-413	7	12
α-helix	421	1
β-strand	422-427	6	12
α-helix	430-432	3
β-strand	434-442	9	12
β-strand	445-450	6	13
β-strand	458-462	5	14
β-strand	473-477	5	14
β-strand	482-486	5	14
β-strand	492-493	2	14
β-strand	507-510	4	15
β-strand	516-520	5	15
β-strand	523-527	5	15
β-strand	533-537	5	15
α-helix	538	1
β-strand	544-549	6	16
β-strand	553-558	6	16
β-strand	562-568	7	16
β-strand	574-576	3	16
β-strand	581-582	2	16
α-helix	583	1
β-strand	587-592	6	17
α-helix	593-596	4
β-strand	604-609	6	17
β-strand	613-618	6	17
β-strand	626-632	7	17
β-strand	637-644	8	18
β-strand	663-669	7	18
β-strand	673-679	7	18
β-strand	683-690	8	18
β-strand	700-706	7	19
β-strand	709-715	7	19
β-strand	719-724	6	19
β-strand	729-733	5	19
β-strand	734	1	12
β-strand	741-745	5	13
β-strand	753-758	6	13
β-strand	761-766	6	13
β-strand	772-780	9	12
β-strand	785-790	6	20
β-strand	797-804	8	20
β-strand	806	1	21
α-helix	809-824	16
α-helix	835-844	10
β-strand	856	1	21
β-strand	862-869	8	20
β-strand	876-881	6	20
β-strand	886-894	9	22
β-strand	904-911	8	22
β-strand	914	1	23
β-strand	919	1	23
β-strand	922-928	7	22
α-helix	931-934	4
β-strand	936	1	24
β-strand	939-945	7	22
β-strand	949-955	7	25
β-strand	958-963	6	25
β-strand	966-971	6	25
β-strand	978-983	6	25
β-strand	990-994	5	26
β-strand	999-1004	6	26
β-strand	1009-1015	7	26
β-strand	1020-1027	8	26
β-strand	1036-1038	3	27
β-strand	1043-1047	5	27
β-strand	1052-1057	6	27
β-strand	1069-1071	3	26
β-strand	1072-1078	7	27
β-strand	1083-1090	8	1
β-strand	1097-1103	7	1
β-strand	1108-1113	6	1
α-helix	1117-1133	17
α-helix	1142-1146	5
β-strand	1153	1	27
β-strand	1155-1157	3	1
α-helix	1158-1161	4
α-helix	1162-1166	5
α-helix	1169-1178	10
α-helix	1183-1197	15
β-strand	1202	1	19

Chain B: 3 helices, 0 β-strands

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

Chain C: 64 helices, 0 β-strands

Element	Residues	Length
α-helix	469-471	3
α-helix	476-478	3
α-helix	494-505	12
α-helix	509-521	13
α-helix	523-526	4
α-helix	528-540	13
α-helix	546-562	17
α-helix	568-570	3
α-helix	571-578	8
α-helix	579-583	5
α-helix	587-603	17
α-helix	606-613	8
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	691-694	4
α-helix	699-716	18
α-helix	722-724	3
α-helix	725-737	13
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	821-823	3
α-helix	827-844	18
α-helix	846-854	9
α-helix	855-858	4
α-helix	862-878	17
α-helix	886-901	16
α-helix	908-921	14
α-helix	922-928	7
α-helix	929-940	12
α-helix	945-963	19
α-helix	968-979	12
α-helix	987-1003	17
α-helix	1013-1020	8
α-helix	1022-1025	4
α-helix	1029-1041	13
α-helix	1042-1046	5
α-helix	1052-1062	11
α-helix	1063-1067	5
α-helix	1071-1088	18
α-helix	1090-1102	13
α-helix	1110-1122	13
α-helix	1125-1137	13
α-helix	1141-1158	18
α-helix	1159-1164	6
α-helix	1166-1177	12
α-helix	1182-1199	18
α-helix	1205-1215	11
α-helix	1216-1219	4
α-helix	1224-1241	18
α-helix	1243-1250	8
α-helix	1252-1254	3
α-helix	1259-1274	16
α-helix	1279-1282	4
α-helix	1284-1286	3
α-helix	1299-1301	3

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	28
β-strand	18-19	2	29
α-helix	20	1
β-strand	21-23	3	30
β-strand	39-42	4	31
α-helix	43	1
β-strand	44-45	2	29
α-helix	52-54	3
β-strand	57	1	32
β-strand	58	1	30
β-strand	64	1	32
β-strand	65-68	4	30
β-strand	70-72	3	31
α-helix	73-77	5
α-helix	80-82	3
β-strand	88-90	3	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Splicing factor 3B subunit 3	A	protein	1209	Homo sapiens	Q15393 (AlphaFold model)
Splicing factor 3B subunit 5	B	protein	85	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

>6EN4_1 Splicing factor 3B subunit 3 (chains A)
VDMFLYNLTLQRATGISFAIHGNFSGTKQQEIVVSRGKILELLRPDPNTGKVHTLLTVEV
FGVIRSLMAFRLTGGTKDYIVVGSDSGRIVILEYQPSKNMFEKIHQETFGKSGCRRIVPG
QFLAVDPKGRAVMISAIEKQKLVYILNRDAAARLTISSPLEAHKANTLVYHVVGVDVGFE
NPMFACLEMDYEEADNDPTGEAAANTQQTLTFYELDLGLNHVVRKYSEPLEEHGNFLITV
PGGSDGPSGVLICSENYITYKNFGDQPDIRCPIPRRRNDLDDPERGMIFVCSATHKTKSM
FFFLAQTEQGDIFKITLETDEDMVTEIRLKYFDTVPVAAAMCVLKTGFLFVASEFGNHYL
YQIAHLGDDDEEPEFSSAMPLEEGDTFFFQPRPLKNLVLVDELDSLSPILFCQIADLANE
DTPQLYVACGRGPRSSLRVLRHGLEVSEMAVSELPGNPNAVWTVRRHIEDEFDAYIIVSF
VNATLVLSIGETVEEVTDSGFLGTTPTLSCSLLGDDALVQVYPDGIRHIRADKRVNEWKT
PGKKTIVKCAVNQRQVVIALTGGELVYFEMDPSGQLNEYTERKEMSADVVCMSLANVPPG
EQRSRFLAVGLVDNTVRIISLDPSDCLQPLSMQALPAQPESLCIVEMGGTEKQDELGERG
SIGFLYLNIGLQNGVLLRTVLDPVTGDLSDTRTRYLGSRPVKLFRVRMQGQEAVLAMSSR
SWLSYSYQSRFHLTPLSYETLEFASGFASEQCPEGIVAISTNTLRILALEKLGAVFNQVA
FPLQYTPRKFVIHPESNNLIIIETDHNAYTEATKAQRKQQMAEEMVEAAGEDERELAAEM
AAAFLNENLPESIFGAPKAGNGQWASVIRVMNPIQGNTLDLVQLEQNEAAFSVAVCRFSN
TGEDWYVLVGVAKDLILNPRSVAGGFVYTYKLVNNGEKLEFLHKTPVEEVPAAIAPFQGR
VLIGVGKLLRVYDLGKKKLLRKCENKHIANYISGIQTIGHRVIVSDVQESFIWVRYKRNE
NQLIIFADDTYPRWVTTASLLDYDTVAGADKFGNICVVRLPPNTNDEVDSQKAEVIMNYH
VGETVLSLQKTTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLRSEHPPLC
GRDHLSFRSYYFPVKNVIDGDLCEQFNSMEPNKQKNVSEELDRTPPEVSKKLEDIRTRYA
FDYKDDDDK

Sequence of entity 2 (B), FASTA

>6EN4_2 Splicing factor 3B subunit 5 (chains B)
TDRYTIHSQLEHLQSKYIGTGHADTTKWEWLVNQHRDSYCSYMGHFDLLNYFAIAENESK
ARVRFNLMEKMLQPCGPPADKPEEN

Sequence of entity 3 (C), FASTA

>6EN4_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

>6EN4_4 PHD finger-like domain-containing protein 5A (chains D)
GPLGSPGSRAMAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECN
YGSYQGRCVICGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDL

Ligands and cofactors

ID	Name	Formula	Copies
BGZ	[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{S})-6-m…	C30 H48 O8	1
ZN	Zinc ion	Zn	3

Primary citation

Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Cretu, C., Agrawal, A.A., Cook, A. et al. Mol Cell (2018) 70:265-273.e8. DOI 10.1016/j.molcel.2018.03.011 · 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)

Browse structure collections

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