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- EMDB-61982: Structure of the SF3B core, harboring the K700E mutation in SF3B1... -

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Entry
Database: EMDB / ID: EMD-61982
TitleStructure of the SF3B core, harboring the K700E mutation in SF3B1, in complex with intron-U2 snRNA
Map data
Sample
  • Complex: SF3B core with K700E mutation in SF3B1 complexed with intron-U2 snRNA
    • 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
    • Protein or peptide: Splicing factor 3B subunit 5
    • RNA: pre-mRNA intron
    • RNA: U2 snRNA
  • Ligand: ZINC ION
KeywordsmRNA splicing / K700E mutation / SPLICING/RNA / SPLICING-RNA complex
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / SAGA complex / U2 snRNP ...U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / SAGA complex / U2 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / regulation of RNA splicing / mRNA Splicing - Minor Pathway / U2 snRNA binding / regulation of DNA repair / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / mRNA splicing, via spliceosome / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / nuclear matrix / nuclear speck / chromatin remodeling / mRNA binding / 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
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 / : / PPP2R1A-like HEAT repeat ...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 / : / PPP2R1A-like HEAT repeat / 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 / 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: 3.5 Å
AuthorsZhang Y / Yin C / Huang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2025
Title: A common structural mechanism for RNA recognition by the SF3B complex in mRNA splicing and export.
Authors: Yuzhu Zhang / Changping Yin / Yimin Wang / Kunming Yan / Bo Zhao / Xin Hu / Youzhong Wan / Hong Cheng / Jing Huang /
Abstract: The SF3B complex plays a critical role in branch point adenosine recognition during pre-mRNA splicing. Its largest subunit SF3B1 is frequently mutated in cancers, leading to aberrant alternative ...The SF3B complex plays a critical role in branch point adenosine recognition during pre-mRNA splicing. Its largest subunit SF3B1 is frequently mutated in cancers, leading to aberrant alternative splicing. Besides its function in pre-mRNA splicing, the SF3B complex also binds mature or intronless mRNAs to facilitate their nuclear export. Notably, the RNA motifs recognized by the SF3B complex exhibit no apparent sequence similarities, raising the question of how the SF3B complex recognizes diverse mRNA sequences for various cellular activities. Here we report the cryo-EM structures of the human SF3B complex associated with either intronless histone mRNAs or intron-U2 snRNA. These structures unveil that both mRNA molecules adopt a similar conformation featuring a bulged adenosine and bind the SF3B complex in a remarkably resembling manner, suggesting that SF3B recognizes the specific shape rather than the sequence of its RNA targets. Further cryo-EM and molecular dynamics analyses of the hotspot-mutant SF3B complexes bound to intron-U2 snRNA demonstrate that the SF3B1K700E and SF3B1R625H mutations similarly repel the attachment of the intronic polypyrimidine tract around the mutation sites, leading to reduced RNA-binding affinity. Altogether, our study provides structural insights into the RNA-recognition mechanism of the SF3B complex and suggests that the cancer-associated SF3B1 mutations could potentially affect multiple cellular processes including mRNA splicing and export, which advances our understanding of the pathogenic mechanisms of the SF3B1 mutations.
History
DepositionOct 16, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61982.png

Downloads & links

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Map

FileDownload / File: emd_61982.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 270 pix.
= 297. Å		1.1 Å/pix.
x 270 pix.
= 297. Å		1.1 Å/pix.
x 270 pix.
= 297. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.188421 - 0.28499722
Average (Standard dev.)0.000090901965 (±0.008916136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61982_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_61982_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_61982_half_map_2.map
Projections & Slices
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Sample components

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Entire : SF3B core with K700E mutation in SF3B1 complexed with intron-U2 snRNA

EntireName: SF3B core with K700E mutation in SF3B1 complexed with intron-U2 snRNA
Components
  • Complex: SF3B core with K700E mutation in SF3B1 complexed with intron-U2 snRNA
    • 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
    • Protein or peptide: Splicing factor 3B subunit 5
    • RNA: pre-mRNA intron
    • RNA: U2 snRNA
  • Ligand: ZINC ION

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Supramolecule #1: SF3B core with K700E mutation in SF3B1 complexed with intron-U2 snRNA

SupramoleculeName: SF3B core with K700E mutation in SF3B1 complexed with intron-U2 snRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Splicing factor 3B subunit 1

MacromoleculeName: Splicing factor 3B subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.192609 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSDLEVLFQ GPLGSMKSVN DQPSGNLPFL KPDDIQYFDK LLVDVDESTL SPEEQKERK IMKLLLKIKN GTPPMRKAAL RQITDKAREF GAGPLFNQIL PLLMSPTLED QERHLLVKVI DRILYKLDDL V RPYVHKIL ...String:
MASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSDLEVLFQ GPLGSMKSVN DQPSGNLPFL KPDDIQYFDK LLVDVDESTL SPEEQKERK IMKLLLKIKN GTPPMRKAAL RQITDKAREF GAGPLFNQIL PLLMSPTLED QERHLLVKVI DRILYKLDDL V RPYVHKIL VVIEPLLIDE DYYARVEGRE IISNLAKAAG LATMISTMRP DIDNMDEYVR NTTARAFAVV ASALGIPSLL PF LKAVCKS KKSWQARHTG IKIVQQIAIL MGCAILPHLR SLVEIIEHGL VDEQQEVRTI SALAIAALAE AATPYGIESF DSV LKPLWK GIRQHRGKGL AAFLKAIGYL IPLMDAEYAN YYTREVMLIL IREFQSPDEE MKKIVLKVVK QCCGTDGVEA NYIK TEILP PFFKHFWQHR MALDRRNYRQ LVDTTVELAN KVGAAEIISR IVDDLKDEAE QYRKMVMETI EKIMGNLGAA DIDHK LEEQ LIDGILYAFQ EQTTEDSVML NGFGTVVNAL GKRVKPYLPQ ICGTVLWRLN NKSAKVRQQA ADLISRTAVV MKTCQE EKL MGHLGVVLYE YLGEEYPEVL GSILGALKAI VNVIGMHKMT PPIKDLLPRL TPILKNRHEK VQENCIDLVG RIADRGA EY VSAREWMRIC FELLELLKAH KKAIRRATVN TFGYIAKAIG PHDVLATLLN NLKVQERQNR VCTTVAIAIV AETCSPFT V LPALMNEYRV PELNVQNGVL KSLSFLFEYI GEMGKDYIYA VTPLLEDALM DRDLVHRQTA SAVVQHMSLG VYGFGCEDS LNHLLNYVWP NVFETSPHVI QAVMGALEGL RVAIGPCRML QYCLQGLFHP ARKVRDVYWK IYNSIYIGSQ DALIAHYPRI YNDDKNTYI RYELDYIL

UniProtKB: Splicing factor 3B subunit 1

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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
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #3: Splicing factor 3B subunit 3

MacromoleculeName: Splicing factor 3B subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.678891 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHMFL YNLTLQRATG ISFAIHGNFS GTKQQEIVVS RGKILELLRP DPNTGKVHTL LTVEVFGVIR SLMAFRLTGG TKDYIVVGS DSGRIVILEY QPSKNMFEKI HQETFGKSGC RRIVPGQFLA VDPKGRAVMI SAIEKQKLVY ILNRDAAARL T ISSPLEAH ...String:
MHHHHHHMFL YNLTLQRATG ISFAIHGNFS GTKQQEIVVS RGKILELLRP DPNTGKVHTL LTVEVFGVIR SLMAFRLTGG TKDYIVVGS DSGRIVILEY QPSKNMFEKI HQETFGKSGC RRIVPGQFLA VDPKGRAVMI SAIEKQKLVY ILNRDAAARL T ISSPLEAH KANTLVYHVV GVDVGFENPM FACLEMDYEE ADNDPTGEAA ANTQQTLTFY ELDLGLNHVV RKYSEPLEEH GN FLITVPG GSDGPSGVLI CSENYITYKN FGDQPDIRCP IPRRRNDLDD PERGMIFVCS ATHKTKSMFF FLAQTEQGDI FKI TLETDE DMVTEIRLKY FDTVPVAAAM CVLKTGFLFV ASEFGNHYLY QIAHLGDDDE EPEFSSAMPL EEGDTFFFQP RPLK NLVLV DELDSLSPIL FCQIADLANE DTPQLYVACG RGPRSSLRVL RHGLEVSEMA VSELPGNPNA VWTVRRHIED EFDAY IIVS FVNATLVLSI GETVEEVTDS GFLGTTPTLS CSLLGDDALV QVYPDGIRHI RADKRVNEWK TPGKKTIVKC AVNQRQ VVI ALTGGELVYF EMDPSGQLNE YTERKEMSAD VVCMSLANVP PGEQRSRFLA VGLVDNTVRI ISLDPSDCLQ PLSMQAL PA QPESLCIVEM GGTEKQDELG ERGSIGFLYL NIGLQNGVLL RTVLDPVTGD LSDTRTRYLG SRPVKLFRVR MQGQEAVL A MSSRSWLSYS YQSRFHLTPL SYETLEFASG FASEQCPEGI VAISTNTLRI LALEKLGAVF NQVAFPLQYT PRKFVIHPE SNNLIIIETD HNAYTEATKA QRKQQMAEEM VEAAGEDERE LAAEMAAAFL NENLPESIFG APKAGNGQWA SVIRVMNPIQ GNTLDLVQL EQNEAAFSVA VCRFSNTGED WYVLVGVAKD LILNPRSVAG GFVYTYKLVN NGEKLEFLHK TPVEEVPAAI A PFQGRVLI GVGKLLRVYD LGKKKLLRKC ENKHIANYIS GIQTIGHRVI VSDVQESFIW VRYKRNENQL IIFADDTYPR WV TTASLLD YDTVAGADKF GNICVVRLPP NTNDEVDEDP TGNKALWDRG LLNGASQKAE VIMNYHVGET VLSLQKTTLI PGG SESLVY TTLSGGIGIL VPFTSHEDHD FFQHVEMHLR SEHPPLCGRD HLSFRSYYFP VKNVIDGDLC EQFNSMEPNK QKNV SEELD RTPPEVSKKL EDIRTRYAF

UniProtKB: Splicing factor 3B subunit 3

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Macromolecule #4: Splicing factor 3B subunit 5

MacromoleculeName: Splicing factor 3B subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.149369 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MTDRYTIHSQ LEHLQSKYIG TGHADTTKWE WLVNQHRDSY CSYMGHFDLL NYFAIAENES KARVRFNLME KMLQPCGPPA DKPEEN

UniProtKB: Splicing factor 3B subunit 5

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Macromolecule #5: pre-mRNA intron

MacromoleculeName: pre-mRNA intron / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.718358 KDa
SequenceString:
GAACAGAUAC UGACACAGUC CCUUUUUUUU CCAC

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Macromolecule #6: U2 snRNA

MacromoleculeName: U2 snRNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.705339 KDa
SequenceString:
GUGUAGUAUC UGUUCUUG

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62574
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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