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- EMDB-6915: SF3b spliceosomal complex bound to E7107 -

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Basic information

Entry
Database: EMDB / ID: EMD-6915
TitleSF3b spliceosomal complex bound to E7107
Map data
Sample
  • Complex: SF3b Sub-complex
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 1
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Protein or peptide: Splicing factor 3B subunit 3
  • Ligand: ZINC ION
  • Ligand: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate
  • Ligand: POTASSIUM IONPotassium
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / regulation of DNA repair / U2 snRNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / mRNA splicing, via spliceosome / nuclear matrix / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term ...Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Splicing factor 3B subunit 1 / Splicing factor 3B subunit 3 / PHD finger-like domain-containing protein 5A / Splicing factor 3B subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsFinci LI / Larsen NA
Funding support China, 1 items
OrganizationGrant numberCountry
NSFC31650110470 China
CitationJournal: Genes Dev / Year: 2018
Title: The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action.
Authors: Lorenzo I Finci / Xiaofeng Zhang / Xiuliang Huang / Qiang Zhou / Jennifer Tsai / Teng Teng / Anant Agrawal / Betty Chan / Sean Irwin / Craig Karr / Andrew Cook / Ping Zhu / Dominic Reynolds ...Authors: Lorenzo I Finci / Xiaofeng Zhang / Xiuliang Huang / Qiang Zhou / Jennifer Tsai / Teng Teng / Anant Agrawal / Betty Chan / Sean Irwin / Craig Karr / Andrew Cook / Ping Zhu / Dominic Reynolds / Peter G Smith / Peter Fekkes / Silvia Buonamici / Nicholas A Larsen /
Abstract: Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted ...Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1 and PHF5A The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure-activity relationship (SAR) on the PHF5A mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.
History
DepositionFeb 23, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseMar 21, 2018-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zya
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6915.png

Downloads & links

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Map

FileDownload / File: emd_6915.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.322 Å
Density
Contour LevelBy AUTHOR: 0.0244 / Movie #1: 0.0244
Minimum - Maximum-0.1155377 - 0.20287405
Average (Standard dev.)0.000100143414 (±0.006705009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin001
Dimensions200200200
Spacing200200200
CellA=B=C: 264.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3221.3221.322
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.400264.400264.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS001
NC/NR/NS200200200
D min/max/mean-0.1160.2030.000

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Supplemental data

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Mask #1

Fileemd_6915_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SF3b Sub-complex

EntireName: SF3b Sub-complex
Components
  • Complex: SF3b Sub-complex
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 1
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • Protein or peptide: Splicing factor 3B subunit 3
  • Ligand: ZINC ION
  • Ligand: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: SF3b Sub-complex

SupramoleculeName: SF3b Sub-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.149369 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

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Macromolecule #2: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146.024938 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKIAKTHED IEAQIREIQG KKAALDEAQG VGLDSTGYYD QEIYGGSDSR FAGYVTSIAA TELEDDDDDY SSSTSLLGQK KPGYHAPVA LLNDIPQSTE QYDPFAEHRP PKIADREDEY KKHRRTMIIS PERLDPFADG GKTPDPKMNA RTYMDVMREQ H LTKEEREI ...String:
MAKIAKTHED IEAQIREIQG KKAALDEAQG VGLDSTGYYD QEIYGGSDSR FAGYVTSIAA TELEDDDDDY SSSTSLLGQK KPGYHAPVA LLNDIPQSTE QYDPFAEHRP PKIADREDEY KKHRRTMIIS PERLDPFADG GKTPDPKMNA RTYMDVMREQ H LTKEEREI RQQLAEKAKA GELKVVNGAA ASQPPSKRKR RWDQTADQTP GATPKKLSSW DQAETPGHTP SLRWDETPGR AK GSETPGA TPGSKIWDPT PSHTPAGAAT PGRGDTPGHA TPGHGGATSS ARKNRWDETP KTERDTPGHG SGWAETPRTD RGG DSIGET PTPGASKRKS RWDETPASQM GGSTPVLTPG KTPIGTPAMN MATPTPGHIM SMTPEQLQAW RWEREIDERN RPLS DEELD AMFPEGYKVL PPPAGYVPIR TPARKLTATP TPLGGMTGFH MQTEDRTMKS VNDQPSGNLP FLKPDDIQYF DKLLV DVDE STLSPEEQKE RKIMKLLLKI KNGTPPMRKA ALRQITDKAR EFGAGPLFNQ ILPLLMSPTL EDQERHLLVK VIDRIL YKL DDLVRPYVHK ILVVIEPLLI DEDYYARVEG REIISNLAKA AGLATMISTM RPDIDNMDEY VRNTTARAFA VVASALG IP SLLPFLKAVC KSKKSWQARH TGIKIVQQIA ILMGCAILPH LRSLVEIIEH GLVDEQQKVR TISALAIAAL AEAATPYG I ESFDSVLKPL WKGIRQHRGK GLAAFLKAIG YLIPLMDAEY ANYYTREVML ILIREFQSPD EEMKKIVLKV VKQCCGTDG VEANYIKTEI LPPFFKHFWQ HRMALDRRNY RQLVDTTVEL ANKVGAAEII SRIVDDLKDE AEQYRKMVME TIEKIMGNLG AADIDHKLE EQLIDGILYA FQEQTTEDSV MLNGFGTVVN ALGKRVKPYL PQICGTVLWR LNNKSAKVRQ QAADLISRTA V VMKTCQEE KLMGHLGVVL YEYLGEEYPE VLGSILGALK AIVNVIGMHK MTPPIKDLLP RLTPILKNRH EKVQENCIDL VG RIADRGA EYVSAREWMR ICFELLELLK AHKKAIRRAT VNTFGYIAKA IGPHDVLATL LNNLKVQERQ NRVCTTVAIA IVA ETCSPF TVLPALMNEY RVPELNVQNG VLKSLSFLFE YIGEMGKDYI YAVTPLLEDA LMDRDLVHRQ TASAVVQHMS LGVY GFGCE DSLNHLLNYV WPNVFETSPH VIQAVMGALE GLRVAIGPCR MLQYCLQGLF HPARKVRDVY WKIYNSIYIG SQDAL IAHY PRIYNDDKNT YIRYELDYIL

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Macromolecule #3: PHD finger-like domain-containing protein 5A

MacromoleculeName: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.394955 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
DLIFCRKQAG VAIGRLCEKC DGKCVICDSY VRPCTLVRIC DECNYGSYQG RCVICGGPGV SDAYYCKECT IQEKDRDGCP KIVNL

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Macromolecule #4: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.471562 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DMFLYNLTLQ RATGISFAIH GNFSGTKQQE IVVSRGKILE LLRPDPNTGK VHTLLTVEVF GVIRSLMAFR LTGGTKDYIV VGSDSGRIV ILEYQPSKNM FEKIHQETFG KSGCRRIVPG QFLAVDPKGR AVMISAIEKQ KLVYILNRDA AARLTISSPL E AHKANTLV ...String:
DMFLYNLTLQ RATGISFAIH GNFSGTKQQE IVVSRGKILE LLRPDPNTGK VHTLLTVEVF GVIRSLMAFR LTGGTKDYIV VGSDSGRIV ILEYQPSKNM FEKIHQETFG KSGCRRIVPG QFLAVDPKGR AVMISAIEKQ KLVYILNRDA AARLTISSPL E AHKANTLV YHVVGVDVGF ENPMFACLEM DYEEADNDPT GEAAANTQQT LTFYELDLGL NHVVRKYSEP LEEHGNFLIT VP GGSDGPS GVLICSENYI TYKNFGDQPD IRCPIPRRRN DLDDPERGMI FVCSATHKTK SMFFFLAQTE QGDIFKITLE TDE DMVTEI RLKYFDTVPV AAAMCVLKTG FLFVASEFGN HYLYQIAHLG DDDEEPEFSS AMPLEEGDTF FFQPRPLKNL VLVD ELDSL SPILFCQIAD LANEDTPQLY VACGRGPRSS LRVLRHGLEV SEMAVSELPG NPNAVWTVRR HIEDEFDAYI IVSFV NATL VLSIGETVEE VTDSGFLGTT PTLSCSLLGD DALVQVYPDG IRHIRADKRV NEWKTPGKKT IVKCAVNQRQ VVIALT GGE LVYFEMDPSG QLNEYTERKE MSADVVCMSL ANVPPGEQRS RFLAVGLVDN TVRIISLDPS DCLQPLSMQA LPAQPES LC IVEMGGTEKQ DELGERGSIG FLYLNIGLQN GVLLRTVLDP VTGDLSDTRT RYLGSRPVKL FRVRMQGQEA VLAMSSRS W LSYSYQSRFH LTPLSYETLE FASGFASEQC PEGIVAISTN TLRILALEKL GAVFNQVAFP LQYTPRKFVI HPESNNLII IETDHNAYTE ATKAQRKQQM AEEMVEAAGE DERELAAEMA AAFLNENLPE SIFGAPKAGN GQWASVIRVM NPIQGNTLDL VQLEQNEAA FSVAVCRFSN TGEDWYVLVG VAKDLILNPR SVAGGFVYTY KLVNNGEKLE FLHKTPVEEV PAAIAPFQGR V LIGVGKLL RVYDLGKKKL LRKCENKHIA NYISGIQTIG HRVIVSDVQE SFIWVRYKRN ENQLIIFADD TYPRWVTTAS LL DYDTVAG ADKFGNICVV RLPPNTNDEV DEDPTGNKAL WDRGLLNGAS QKAEVIMNYH VGETVLSLQK TTLIPGGSES LVY TTLSGG IGILVPFTSH EDHDFFQHVE MHLRSEHPPL CGRDHLSFRS YYFPVKNVID GDLCEQFNSM EPNKQKNVSE ELDR TPPEV SKKLEDIRTR YAFDYKDD

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~...

MacromoleculeName: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10- ...Name: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate
type: ligand / ID: 6 / Number of copies: 1 / Formula: 9B0
Molecular weightTheoretical: 718.96 Da
Chemical component information

ChemComp-9B0:
[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate

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Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ife

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241288

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