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- EMDB-74089: Cryo-EM structure of the endogenous U2/branchpoint spliceosomal c... -

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Basic information

Entry
Database: EMDB / ID: EMD-74089
TitleCryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core)
Map data
Sample
  • Complex: Endogenous U2/branchpoint spliceosomal complex (Core)
    • RNA: x 2 types
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
Keywordsspliceosome / tumor suppressor / helicase / DHX15 / RBM5 / SR140 / prespliceosomal A complex / SPLICING
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / splicing factor binding / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2-type spliceosomal complex / SAGA complex ...U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / splicing factor binding / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2-type spliceosomal complex / SAGA complex / U2 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / perinuclear theca / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / mRNA 3'-splice site recognition / regulation of RNA splicing / mRNA Splicing - Minor Pathway / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / U2 snRNA binding / regulation of DNA repair / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / sperm end piece / centriole / mRNA splicing, via spliceosome / positive regulation of neuron projection development / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / nuclear matrix / mRNA processing / sperm principal piece / sperm midpiece / nuclear speck / positive regulation of apoptotic process / chromatin remodeling / negative regulation of cell population proliferation / mRNA binding / apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / SF3B6, RNA recognition motif / SF3B4, RNA recognition motif 2 / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Cactus-binding C-terminus of cactin protein / : ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / SF3B6, RNA recognition motif / SF3B4, RNA recognition motif 2 / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Cactus-binding C-terminus of cactin protein / : / Replication stress response SDE2 C-terminal / G-patch domain / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / G-patch domain profile. / SF3B4, RNA recognition motif 1 / : / G-patch domain / glycine rich nucleic binding domain / : / : / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Zinc-finger of C2H2 type / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / 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 / : / PPP2R1A-like HEAT repeat / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Splicing factor 3B subunit 1 / RNA-binding protein 5 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / Splicing factor 3A subunit 2 / PHD finger-like domain-containing protein 5A / Splicing factor 3B subunit 5 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsLiu S / Su T / Zhou ZH
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UCLA CTSI Grant UL1TR001881 United States
CitationJournal: bioRxiv / Year: 2026
Title: The tumour suppressor RBM5 activates the helicase DHX15 to regulate splicing.
Authors: Shiheng Liu / Tiantian Su / Jeffrey Huang / Chia-Ho Lin / Douglas L Black / Andrey Damianov / Z Hong Zhou
Abstract: Pre-mRNA splicing determines the expressed proteome and is frequently dysregulated in cancer. The tumour-suppressor RBM5 controls an exon network regulating apoptosis, yet its molecular mechanism is ...Pre-mRNA splicing determines the expressed proteome and is frequently dysregulated in cancer. The tumour-suppressor RBM5 controls an exon network regulating apoptosis, yet its molecular mechanism is elusive. Using in vivo spliceosome capture and cryogenic electron microscopy, we determined structures of precatalytic spliceosomes arrested by RBM5 immediately after U2 snRNP branchpoint recognition. Despite intron diversity, the U2-pre-mRNA duplex, branchpoint adenine, and downstream polypyrimidine tract are well-resolved. RBM5 binds the outer SF3B1 HEAT surface and performs dual functions: First, its helix-loop-helix motif and upstream zinc-finger domain sterically block tri-snRNP and Prp8 docking and prevent progression to pre-B and B complexes; Second, its G-patch activates DHX15 and places this DExH-box helicase on the pre-mRNA as it exits SF3B1, poised for branch helix unwinding. DHX15 binding to SF3B1 is facilitated by U2SURP/SR140, which engages SF3B1 near RBM5's helix-loop-helix. Functional assays confirm that disruption of the RBM5 interfaces with either DHX15 or SF3B1 inhibit exon repression. Mutations at these regulatory interfaces are common in cancer genomes and predicted to disrupt its regulation of apoptotic isoforms. Thus, RBM5 acts as a dual-action spliceosome gatekeeper that couples helicase activation with physical stalling to enforce tumour-suppressive alternative splicing programmes.
History
DepositionNov 27, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74089.png

Downloads & links

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Map

FileDownload / File: emd_74089.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.72
Minimum - Maximum-2.7172163 - 4.200224
Average (Standard dev.)0.0026221299 (±0.07571069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The sharpened map was processed with EMReady2 to aid model building

Fileemd_74089_additional_1.map
AnnotationThe sharpened map was processed with EMReady2 to aid model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74089_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74089_half_map_2.map
Projections & Slices
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Sample components

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Entire : Endogenous U2/branchpoint spliceosomal complex (Core)

EntireName: Endogenous U2/branchpoint spliceosomal complex (Core)
Components
  • Complex: Endogenous U2/branchpoint spliceosomal complex (Core)
    • RNA: U2 snRNA
    • Protein or peptide: PHD finger-like domain-containing protein 5A
    • RNA: pre-mRNA
    • Protein or peptide: RNA-binding protein 5
    • Protein or peptide: Splicing factor 3B subunit 1
    • Protein or peptide: Splicing factor 3B subunit 2
    • Protein or peptide: Splicing factor 3B subunit 3
    • Protein or peptide: Splicing factor 3B subunit 4
    • Protein or peptide: Splicing factor 3B subunit 5
    • Protein or peptide: Splicing factor 3B subunit 6
    • Protein or peptide: Splicing factor 3A subunit 2
    • Protein or peptide: Splicing factor 3A subunit 3
  • Ligand: ZINC ION

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Supramolecule #1: Endogenous U2/branchpoint spliceosomal complex (Core)

SupramoleculeName: Endogenous U2/branchpoint spliceosomal complex (Core) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: U2 snRNA

MacromoleculeName: U2 snRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.784973 KDa
SequenceString:
AAGUG(PSU)AG(PSU)A (PSU)(OMC)(PSU)G(PSU)(PSU)CU(OMC)A UCAGU(PSU)UAA(PSU) AU(OMC)UGA U

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Macromolecule #3: pre-mRNA

MacromoleculeName: pre-mRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.835073 KDa
SequenceString:
UUUUUUUUUU UUUUUCUCAU UUUUUUUUUU UUUUUUUUUU UU

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Macromolecule #2: PHD finger-like domain-containing protein 5A

MacromoleculeName: PHD finger-like domain-containing protein 5A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.427524 KDa
SequenceString:
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIV NLGSSKTDLF YERKKYGFKK R

UniProtKB: PHD finger-like domain-containing protein 5A

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Macromolecule #4: RNA-binding protein 5

MacromoleculeName: RNA-binding protein 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.410133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSDKRVSRT ERSGRYGSII DRDDRDERES RSRRRDSDYK RSSDDRRGDR YDDYRDYDSP ERERERRNSD RSEDGYHSDG DYGEHDYRH DISDERESKT IMLRGLPITI TESDIREMME SFEGPQPADV RLMKRKTGVS RGFAFVEFYH LQDATSWMEA N QKKLVIQG ...String:
MGSDKRVSRT ERSGRYGSII DRDDRDERES RSRRRDSDYK RSSDDRRGDR YDDYRDYDSP ERERERRNSD RSEDGYHSDG DYGEHDYRH DISDERESKT IMLRGLPITI TESDIREMME SFEGPQPADV RLMKRKTGVS RGFAFVEFYH LQDATSWMEA N QKKLVIQG KHIAMHYSNP RPKFEDWLCN KCCLNNFRKR LKCFRCGADK FDSEQEVPPG TTESVQSVDY YCDTIILRNI AP HTVVDSI MTALSPYASL AVNNIRLIKD KQTQQNRGFA FVQLSSAMDA SQLLQILQSL HPPLKIDGKT IGVDFAKSAR KDL VLSDGN RVSAFSVAST AIAAAQWSST QSQSGEGGSV DYSYLQPGQD GYAQYAQYSQ DYQQFYQQQA GGLESDASSA SGTA VTTTS AAVVSQSPQL YNQTSNPPGS PTEEAQPSTS TSTQAPAASP TGVVPGTKYA VPDTSTYQYD ESSGYYYDPT TGLYY DPNS QYYYNSLTQQ YLYWDGEKET YVPAAESSSH QQSGLPPAKE GKEKKEKPKS KTAQQIAKDM ERWAKSLNKQ KENFKN SFQ PVNSLREEER RESAAADAGF ALFEKKGALA ERQQLIPELV RNGDEENPLK RGLVAAYSGD SDNEEELVER LESEEEK LA DWKKMACLLC RRQFPNKDAL VRHQQLSDLH KQNMDIYRRS RLSEQELEAL ELREREMKYR DRAAERREKY GIPEPPEP K RKKQFDAGTV NYEQPTKDGI DHSNIGNKML QAMGWREGSG LGRKCQGITA PIEAQVRLKG AGLGAKGSAY GLSGADSYK DAVRKAMFAR FTEMEMDYKD DDDK

UniProtKB: RNA-binding protein 5

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Macromolecule #5: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146.024938 KDa
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

UniProtKB: Splicing factor 3B subunit 1

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Macromolecule #6: Splicing factor 3B subunit 2

MacromoleculeName: Splicing factor 3B subunit 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.377812 KDa
SequenceString: MATEHPEPPK AELQLPPPPP PGHYGAWAAQ ELQAKLAEIG APIQGNREEL VERLQSYTRQ TGIVLNRPVL RGEDGDKAAP PPMSAQLPG IPMPPPPLGL PPLQPPPPPP PPPPGLGLGF PMAHPPNLGP PPPLRVGEPV ALSEEERLKL AQQQAALLMQ Q EERAKQQG ...String:
MATEHPEPPK AELQLPPPPP PGHYGAWAAQ ELQAKLAEIG APIQGNREEL VERLQSYTRQ TGIVLNRPVL RGEDGDKAAP PPMSAQLPG IPMPPPPLGL PPLQPPPPPP PPPPGLGLGF PMAHPPNLGP PPPLRVGEPV ALSEEERLKL AQQQAALLMQ Q EERAKQQG DHSLKEHELL EQQKRAAVLL EQERQQEIAK MGTPVPRPPQ DMGQIGVRTP LGPRVAAPVG PVGPTPTVLP MG APVPRPR GPPPPPGDEN REMDDPSVGP KIPQALEKIL QLKESRQEEM NSQQEEEEME TDARSSLGQS ASETEEDTVS VSK KEKNRK RRNRKKKKKP QRVRGVSSES SGDREKDSTR SRGSDSPAAD VEIEYVTEEP EIYEPNFIFF KRIFEAFKLT DDVK KEKEK EPEKLDKLEN SAAPKKKGFE EEHKDSDDDS SDDEQEKKPE APKLSKKKLR RMNRFTVAEL KQLVARPDVV EMHDV TAQD PKLLVHLKAT RNSVPVPRHW CFKRKYLQGK RGIEKPPFEL PDFIKRTGIQ EMREALQEKE EQKTMKSKMR EKVRPK MGK IDIDYQKLHD AFFKWQTKPK LTIHGDLYYE GKEFETRLKE KKPGDLSDEL RISLGMPVGP NAHKVPPPWL IAMQRYG PP PSYPNLKIPG LNSPIPESCS FGYHAGGWGK PPVDETGKPL YGDVFGTNAA EFQTKTEEEE IDRTPWGELE PSDEESSE E EEEEESDEDK PDETGFITPA DSGLITPGGF SSVPAGMETP ELIELRKKKI EEAMDGSETP QLFTVLPEKR TATVGGAMM GSTHIYDMST VMSRKGPAPE LQGVEVALAP EELELDPMAM TQKYEEHVRE QQAQVEKEDF SDMVAEHAAK QKQKKRKAQP QDSRGGSKK YKEFKF

UniProtKB: Splicing factor 3B subunit 2

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Macromolecule #7: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.718844 KDa
SequenceString: MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVI LEYQPSKNMF EKIHQETFGK SGCRRIVPGQ FLAVDPKGRA VMISAIEKQK LVYILNRDAA ARLTISSPLE A HKANTLVY ...String:
MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVI LEYQPSKNMF EKIHQETFGK SGCRRIVPGQ FLAVDPKGRA VMISAIEKQK LVYILNRDAA ARLTISSPLE A HKANTLVY HVVGVDVGFE NPMFACLEMD YEEADNDPTG EAAANTQQTL TFYELDLGLN HVVRKYSEPL EEHGNFLITV PG GSDGPSG VLICSENYIT YKNFGDQPDI RCPIPRRRND LDDPERGMIF VCSATHKTKS MFFFLAQTEQ GDIFKITLET DED MVTEIR LKYFDTVPVA AAMCVLKTGF LFVASEFGNH YLYQIAHLGD DDEEPEFSSA MPLEEGDTFF FQPRPLKNLV LVDE LDSLS PILFCQIADL ANEDTPQLYV ACGRGPRSSL RVLRHGLEVS EMAVSELPGN PNAVWTVRRH IEDEFDAYII VSFVN ATLV LSIGETVEEV TDSGFLGTTP TLSCSLLGDD ALVQVYPDGI RHIRADKRVN EWKTPGKKTI VKCAVNQRQV VIALTG GEL VYFEMDPSGQ LNEYTERKEM SADVVCMSLA NVPPGEQRSR FLAVGLVDNT VRIISLDPSD CLQPLSMQAL PAQPESL CI VEMGGTEKQD ELGERGSIGF LYLNIGLQNG VLLRTVLDPV TGDLSDTRTR YLGSRPVKLF RVRMQGQEAV LAMSSRSW L SYSYQSRFHL TPLSYETLEF ASGFASEQCP EGIVAISTNT LRILALEKLG AVFNQVAFPL QYTPRKFVIH PESNNLIII ETDHNAYTEA TKAQRKQQMA EEMVEAAGED ERELAAEMAA AFLNENLPES IFGAPKAGNG QWASVIRVMN PIQGNTLDLV QLEQNEAAF SVAVCRFSNT GEDWYVLVGV AKDLILNPRS VAGGFVYTYK LVNNGEKLEF LHKTPVEEVP AAIAPFQGRV L IGVGKLLR VYDLGKKKLL RKCENKHIAN YISGIQTIGH RVIVSDVQES FIWVRYKRNE NQLIIFADDT YPRWVTTASL LD YDTVAGA DKFGNICVVR LPPNTNDEVD EDPTGNKALW DRGLLNGASQ KAEVIMNYHV GETVLSLQKT TLIPGGSESL VYT TLSGGI GILVPFTSHE DHDFFQHVEM HLRSEHPPLC GRDHLSFRSY YFPVKNVIDG DLCEQFNSME PNKQKNVSEE LDRT PPEVS KKLEDIRTRY AF

UniProtKB: Splicing factor 3B subunit 3

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Macromolecule #8: Splicing factor 3B subunit 4

MacromoleculeName: Splicing factor 3B subunit 4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.43657 KDa
SequenceString: MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT GQHQGYGFVE FLSEEDADYA IKIMNMIKLY GKPIRVNKA SAHNKNLDVG ANIFIGNLDP EIDEKLLYDT FSAFGVILQT PKIMRDPDTG NSKGYAFINF ASFDASDAAI E AMNGQYLC ...String:
MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT GQHQGYGFVE FLSEEDADYA IKIMNMIKLY GKPIRVNKA SAHNKNLDVG ANIFIGNLDP EIDEKLLYDT FSAFGVILQT PKIMRDPDTG NSKGYAFINF ASFDASDAAI E AMNGQYLC NRPITVSYAF KKDSKGERHG SAAERLLAAQ NPLSQADRPH QLFADAPPPP SAPNPVVSSL GSGLPPPGMP PP GSFPPPV PPPGALPPGI PPAMPPPPMP PGAAGHGPPS AGTPGAGHPG HGHSHPHPFP PGGMPHPGMS QMQLAHHGPH GLG HPHAGP PGSGGQPPPR PPPGMPHPGP PPMGMPPRGP PFGSPMGHPG PMPPHGMRGP PPLMPPHGYT GPPRPPPYGY QRGP LPPPR PTPRPPVPPR GPLRGPLPQ

UniProtKB: Splicing factor 3B subunit 4

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Macromolecule #9: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.149369 KDa
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

UniProtKB: Splicing factor 3B subunit 5

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Macromolecule #10: Splicing factor 3B subunit 6

MacromoleculeName: Splicing factor 3B subunit 6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.6069 KDa
SequenceString:
MAMQAAKRAN IRLPPEVNRI LYIRNLPYKI TAEEMYDIFG KYGPIRQIRV GNTPETRGTA YVVYEDIFDA KNACDHLSGF NVCNRYLVV LYYNANRAFQ KMDTKKKEEQ LKLLKEKYGI NTDPPK

UniProtKB: Splicing factor 3B subunit 6

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Macromolecule #11: Splicing factor 3A subunit 2

MacromoleculeName: Splicing factor 3A subunit 2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.327355 KDa
SequenceString: MDFQHRPGGK TGSGGVASSS ESNRDRRERL RQLALETIDI NKDPYFMKNH LGSYECKLCL TLHNNEGSYL AHTQGKKHQT NLARRAAKE AKEAPAQPAP EKVKVEVKKF VKIGRPGYKV TKQRDSEMGQ QSLLFQIDYP EIAEGIMPRH RFMSAYEQRI E PPDRRWQY ...String:
MDFQHRPGGK TGSGGVASSS ESNRDRRERL RQLALETIDI NKDPYFMKNH LGSYECKLCL TLHNNEGSYL AHTQGKKHQT NLARRAAKE AKEAPAQPAP EKVKVEVKKF VKIGRPGYKV TKQRDSEMGQ QSLLFQIDYP EIAEGIMPRH RFMSAYEQRI E PPDRRWQY LLMAAEPYET IAFKVPSREI DKAEGKFWTH WNRETKQFFL QFHFKMEKPP APPSLPAGPP GVKRPPPPLM NG LPPRPPL PESLPPPPPG GLPLPPMPPT GPAPSGPPGP PQLPPPAPGV HPPAPVVHPP ASGVHPPAPG VHPPAPGVHP PAP GVHPPT SGVHPPAPGV HPPAPGVHPP APGVHPPAPG VHPPAPGVHP PPSAGVHPQA PGVHPAAPAV HPQAPGVHPP APGM HPQAP GVHPQPPGVH PSAPGVHPQP PGVHPSNPGV HPPTPMPPML RPPLPSEGPG NIPPPPPTN

UniProtKB: Splicing factor 3A subunit 2

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Macromolecule #12: Splicing factor 3A subunit 3

MacromoleculeName: Splicing factor 3A subunit 3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.934844 KDa
SequenceString: METILEQQRR YHEEKERLMD VMAKEMLTKK STLRDQINSD HRTRAMQDRY MEVSGNLRDL YDDKDGLRKE ELNAISGPNE FAEFYNRLK QIKEFHRKHP NEICVPMSVE FEELLKAREN PSEEAQNLVE FTDEEGYGRY LDLHDCYLKY INLKASEKLD Y ITYLSIFD ...String:
METILEQQRR YHEEKERLMD VMAKEMLTKK STLRDQINSD HRTRAMQDRY MEVSGNLRDL YDDKDGLRKE ELNAISGPNE FAEFYNRLK QIKEFHRKHP NEICVPMSVE FEELLKAREN PSEEAQNLVE FTDEEGYGRY LDLHDCYLKY INLKASEKLD Y ITYLSIFD QLFDIPKERK NAEYKRYLEM LLEYLQDYTD RVKPLQDQNE LFGKIQAEFE KKWENGTFPG WPKETSSALT HA GAHLDLS AFSSWEELAS LGLDRLKSAL LALGLKCGGT LEERAQRLFS TKGKSLESLD TSLFAKNPKS KGTKRDTERN KDI AFLEAQ IYEYVEILGE QRHLTHENVQ RKQARTGEER EEEEEEQISE SESEDEENEI IYNPKNLPLG WDGKPIPYWL YKLH GLNIN YNCEICGNYT YRGPKAFQRH FAEWRHAHGM RCLGIPNTAH FANVTQIEDA VSLWAKLKLQ KASERWQPDT EEEYE DSSG NVVNKKTYED LKRQGLL

UniProtKB: Splicing factor 3A subunit 3

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 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

BufferpH: 7.9
Details: 20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction via CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 128413
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 127.6
Output model

PDB-9ze2:
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core)

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