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- EMDB-13045: Cryo-EM structure of Brr2 in complex with Fbp21 -

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Basic information

Entry
Database: EMDB / ID: EMD-13045
TitleCryo-EM structure of Brr2 in complex with Fbp21
Map data
Sample
  • Complex: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21
    • Complex: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
      • Protein or peptide: U5 small nuclear ribonucleoprotein 200 kDa helicase
    • Complex: WW domain-binding protein 4 (Fbp21)
      • Protein or peptide: WW domain-binding protein 4
KeywordsmRNA Splicing / Spliceosomal Assembly / Splicing Regulation / Brr2 Helicase / SPLICING
Function / homology
Function and homology information


cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / mRNA cis splicing, via spliceosome / 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 / U2-type precatalytic spliceosome / proline-rich region binding / mRNA cis splicing, via spliceosome / precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / 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
WW domain-binding protein 4 / U1-C, C2H2-type zinc finger / U1 zinc finger / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain ...WW domain-binding protein 4 / U1-C, C2H2-type zinc finger / U1 zinc finger / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Zinc finger C2H2 superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
WW domain-binding protein 4 / U5 small nuclear ribonucleoprotein 200 kDa helicase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBergfort A / Hilal T
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR186-A15 Germany
Citation
Journal: Nucleic Acids Res / Year: 2022
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: Journal: Acta Crystallogr D Struct Biol / Year: 2019
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
DepositionJun 7, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7os1
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13045.png

Downloads & links

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Map

FileDownload / File: emd_13045.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 336 pix.
= 279.552 Å		0.83 Å/pix.
x 336 pix.
= 279.552 Å		0.83 Å/pix.
x 336 pix.
= 279.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum0.0 - 2.191979
Average (Standard dev.)0.007986474 (±0.050317716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 279.552 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z279.552279.552279.552
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean0.0002.1920.008

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Supplemental data

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Sample components

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Entire : Dimeric complex of Brr2 and a C-terminal fragment of Fbp21

EntireName: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21
Components
  • Complex: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21
    • Complex: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
      • Protein or peptide: U5 small nuclear ribonucleoprotein 200 kDa helicase
    • Complex: WW domain-binding protein 4 (Fbp21)
      • Protein or peptide: WW domain-binding protein 4

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Supramolecule #1: Dimeric complex of Brr2 and a C-terminal fragment of Fbp21

SupramoleculeName: 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)

SupramoleculeName: U5 small nuclear ribonucleoprotein 200 kDa helicase (Brr2)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: WW domain-binding protein 4 (Fbp21)

SupramoleculeName: WW domain-binding protein 4 (Fbp21) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: U5 small nuclear ribonucleoprotein 200 kDa helicase

MacromoleculeName: U5 small nuclear ribonucleoprotein 200 kDa helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 198.785797 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

UniProtKB: U5 small nuclear ribonucleoprotein 200 kDa helicase

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Macromolecule #2: WW domain-binding protein 4

MacromoleculeName: WW domain-binding protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.208762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMAFNPHTS DLPSSKVNEN SLGTLDESKS SDSHSDSDGE QEAEEGGVST ETEKPKIKFK EKNKNSDGGS DPETQKEKSI QKQNSLGSN EEKSKTLKKS NPYGEWQEIK QEVESHEEVD LELPSTENEY VSTSEADGGG EPKVVFKEKT VTSLGVMADG V APVFKKRR TENGKSRNLR QRGDDQ

UniProtKB: WW domain-binding protein 4

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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

Concentration5 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 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: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
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

Particle selectionNumber selected: 787610
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9) / Number images used: 57854
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.9)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.9)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4kit

chain_id: B, source_name: PDB, initial_model_type: experimental model

4kit

chain_id: C, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 102 / Target criteria: CC, R.m.s.d. Bonds / Angles
Output model

PDB-7os1:
Cryo-EM structure of Brr2 in complex with Fbp21

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