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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13045 | |||||||||
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Title | Cryo-EM structure of Brr2 in complex with Fbp21 | |||||||||
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Function / homology | ![]() cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Bergfort A / Hilal T / Weber G / Wahl MC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling. Authors: Alexandra Bergfort / Tarek Hilal / Benno Kuropka / İbrahim Avşar Ilik / Gert Weber / Tuğçe Aktaş / Christian Freund / Markus C Wahl / ![]() Abstract: Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. ...Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4's intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling. #1: ![]() Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Liebschner D / Afonine PV / Baker ML / Bunkoczi G / Chen VB / Croll TI / Hintze B / Hung LW / Jain S / McCoy AJ / Moriarty NW / Oeffner RD / Poon BK / Prisant MG / Read RJ / Richardson JS / ...Authors: Liebschner D / Afonine PV / Baker ML / Bunkoczi G / Chen VB / Croll TI / Hintze B / Hung LW / Jain S / McCoy AJ / Moriarty NW / Oeffner RD / Poon BK / Prisant MG / Read RJ / Richardson JS / Richardson DC / Sammito MD / Sobolev OV / Stockwell DH / Terwilliger TC / Urzhumtsev AG / Videau LL / Williams CJ / Adams PD | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 37.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 83.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 338.6 KB | Display | ![]() |
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Full document | ![]() | 338.2 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7os1MC ![]() 7os2C ![]() 7px3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Dimeric complex of Brr2 and a C-terminal fragment of Fbp21
Entire | Name: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21 |
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Components |
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-Supramolecule #1: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21
Supramolecule | Name: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
Supramolecule | Name: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2) type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: WW domain-binding protein 4 (Fbp21)
Supramolecule | Name: WW domain-binding protein 4 (Fbp21) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: U5 small nuclear ribonucleoprotein 200 kDa helicase
Macromolecule | Name: U5 small nuclear ribonucleoprotein 200 kDa helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 198.785797 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAEFDLDQGG EALAPRQVLD LEDLVFTQGS HFMANKRCQL PDGSFRRQRK GYEEVHVPAL KPKPFGSEEQ LLPVEKLPKY AQAGFEGFK TLNRIQSKLY RAALETDENL LLCAPTGAGK TNVALMCMLR EIGKHINMDG TINVDDFKII YIAPMRSLVQ E MVGSFGKR ...String: GAEFDLDQGG EALAPRQVLD LEDLVFTQGS HFMANKRCQL PDGSFRRQRK GYEEVHVPAL KPKPFGSEEQ LLPVEKLPKY AQAGFEGFK TLNRIQSKLY RAALETDENL LLCAPTGAGK TNVALMCMLR EIGKHINMDG TINVDDFKII YIAPMRSLVQ E MVGSFGKR LATYGITVAE LTGDHQLCKE EISATQIIVC TPEKWDIITR KGGERTYTQL VRLIILDEIH LLHDDRGPVL EA LVARAIR NIEMTQEDVR LIGLSATLPN YEDVATFLRV DPAKGLFYFD NSFRPVPLEQ TYVGITEKKA IKRFQIMNEI VYE KIMEHA GKNQVLVFVH SRKETGKTAR AIRDMCLEKD TLGLFLREGS ASTEVLRTEA EQCKNLELKD LLPYGFAIHH AGMT RVDRT LVEDLFADKH IQVLVSTATL AWGVNLPAHT VIIKGTQVYS PEKGRWTELG ALDILQMLGR AGRPQYDTKG EGILI TSHG ELQYYLSLLN QQLPIESQMV SKLPDMLNAE IVLGNVQNAK DAVNWLGYAY LYIRMLRSPT LYGISHDDLK GDPLLD QRR LDLVHTAALM LDKNNLVKYD KKTGNFQVTE LGRIASHYYI TNDTVQTYNQ LLKPTLSEIE LFRVFSLSSE FKNITVR EE EKLELQKLLE RVPIPVKESI EEPSAKINVL LQAFISQLKL EGFALMADMV YVTQSAGRLM RAIFEIVLNR GWAQLTDK T LNLCKMIDKR MWQSMCPLRQ FRKLPEEVVK KIEKKNFPFE RLYDLNHNEI GELIRMPKMG KTIHKYVHLF PKLELSVHL QPITRSTLKV ELTITPDFQW DEKVHGSSEA FWILVEDVDS EVILHHEYFL LKAKYAQDEH LITFFVPVFE PLPPQYFIRV VSDRWLSCE TQLPVSFRHL ILPEKYPPPT ELLDLQPLPV SALRNSAFES LYQDKFPFFN PIQTQVFNTV YNSDDNVFVG A PTGSGKTI CAEFAILRML LQSSEGRCVY ITPMEALAEQ VYMDWYEKFQ DRLNKKVVLL TGETSTDLKL LGKGNIIIST PE KWDILSR RWKQRKNVQN INLFVVDEVH LIGGENGPVL EVICSRMRYI SSQIERPIRI VALSSSLSNA KDVAHWLGCS ATS TFNFHP NVRPVPLELH IQGFNISHTQ TRLLSMAKPV YHAITKHSPK KPVIVFVPSR KQTRLTAIDI LTTCAADIQR QRFL HCTEK DLIPYLEKLS DSTLKETLLN GVGYLHEGLS PMERRLVEQL FSSGAIQVVV ASRSLCWGMN VAAHLVIIMD TQYYN GKIH AYVDYPIYDV LQMVGHANRP LQDDEGRCVI MCQGSKKDFF KKFLYEPLPV ESHLDHCMHD HFNAEIVTKT IENKQD AVD YLTWTFLYRR MTQNPNYYNL QGISHRHLSD HLSELVEQTL SDLEQSKCIS IEDEMDVAPL NLGMIAAYYY INYTTIE LF SMSLNAKTKV RGLIEIISNA AEYENIPIRH HEDNLLRQLA QKVPHKLNNP KFNDPHVKTN LLLQAHLSRM QLSAELQS D TEEILSKAIR LIQACVDVLS SNGWLSPALA AMELAQMVTQ AMWSKDSYLK QLPHFTSEHI KRCTDKGVES VFDIMEMED EERNALLQLT DSQIADVARF CNRYPNIELS YEVVDKDSIR SGGPVVVLVQ LEREEEVTGP VIAPLFPQKR EEGWWVVIGD AKSNSLISI KRLTLQQKAK VKLDFVAPAT GAHNYTLYFM SDAYMGCDQE YKFSVDVKEA |
-Macromolecule #2: WW domain-binding protein 4
Macromolecule | Name: WW domain-binding protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.208762 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAMAFNPHTS DLPSSKVNEN SLGTLDESKS SDSHSDSDGE QEAEEGGVST ETEKPKIKFK EKNKNSDGGS DPETQKEKSI QKQNSLGSN EEKSKTLKKS NPYGEWQEIK QEVESHEEVD LELPSTENEY VSTSEADGGG EPKVVFKEKT VTSLGVMADG V APVFKKRR TENGKSRNLR QRGDDQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1877 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |