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- EMDB-18825: Structure of C. thermophilum RNA exosome core -

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Basic information

Entry
Database: EMDB / ID: EMD-18825
TitleStructure of C. thermophilum RNA exosome core
Map data
Sample
  • Complex: RNA exosome core (Exo9)
    • Protein or peptide: Rrp45
    • Protein or peptide: Exoribonuclease phosphorolytic domain-containing protein
    • Protein or peptide: Exoribonuclease-like protein
    • Protein or peptide: Exoribonuclease phosphorolytic domain-containing protein
    • Protein or peptide: Exoribonuclease phosphorolytic domain-containing protein
    • Protein or peptide: Exosome complex component MTR3
    • Protein or peptide: Ribosomal RNA-processing protein 40
    • Protein or peptide: Putative exosome complex protein
    • Protein or peptide: Putative exosome 3'->5 protein
Keywordsnuclease / RNA degradation / RNA metabolism / RNA binding / RNA BINDING PROTEIN
Function / homology
Function and homology information


exosome (RNase complex) / nuclear exosome (RNase complex) / RNA processing / rRNA processing / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 ...Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / : / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / K Homology domain, type 1 / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Ribosomal RNA-processing protein 42 / Ribosomal RNA-processing protein 40 / Ribosomal RNA-processing protein 43 / Uncharacterized protein / Putative exosome complex protein / Uncharacterized protein / Exoribonuclease phosphorolytic domain-containing protein / Putative exosome 3'->5 protein / Exosome complex component MTR3
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLazzaretti D / Liebau J / Pilsl M / Sprangers R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SP 1324/3-1 Germany
CitationJournal: Biorxiv / Year: 2024
Title: Beyond static structures: quantitative dynamics in the eukaryotic RNA exosome complex
Authors: Liebau J / Lazzaretti D / Bichler A / Pilsl M / Sprangers R
History
DepositionNov 2, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18825.png

Downloads & links

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Map

FileDownload / File: emd_18825.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 256 pix.
= 197.632 Å		0.77 Å/pix.
x 256 pix.
= 197.632 Å		0.77 Å/pix.
x 256 pix.
= 197.632 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.772 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0075539066 - 0.019743063
Average (Standard dev.)0.000024314744 (±0.0010618538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 197.632 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Post-processed map (deepEMhancer)

Fileemd_18825_additional_1.map
AnnotationPost-processed map (deepEMhancer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18825_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18825_half_map_2.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 : RNA exosome core (Exo9)

EntireName: RNA exosome core (Exo9)
Components
  • Complex: RNA exosome core (Exo9)
    • Protein or peptide: Rrp45
    • Protein or peptide: Exoribonuclease phosphorolytic domain-containing protein
    • Protein or peptide: Exoribonuclease-like protein
    • Protein or peptide: Exoribonuclease phosphorolytic domain-containing protein
    • Protein or peptide: Exoribonuclease phosphorolytic domain-containing protein
    • Protein or peptide: Exosome complex component MTR3
    • Protein or peptide: Ribosomal RNA-processing protein 40
    • Protein or peptide: Putative exosome complex protein
    • Protein or peptide: Putative exosome 3'->5 protein

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Supramolecule #1: RNA exosome core (Exo9)

SupramoleculeName: RNA exosome core (Exo9) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 294 KDa

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Macromolecule #1: Rrp45

MacromoleculeName: Rrp45 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 32.470098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPREVEPSLS ERQFVLQALQ EGLRLDGRQL DQYRPLSLTF GDQYGVADVT FGKTRVLAKA SAEVTVPYAD RPLDGIFTIA TELSPMTSP TFEVNRPTET EVLLSRLLEK TIRRSGALDT ESLCLVAGQK CWSIRVDVHV MSHDGNLVDA ACIAVVAALR H FRKPDTSI ...String:
MPREVEPSLS ERQFVLQALQ EGLRLDGRQL DQYRPLSLTF GDQYGVADVT FGKTRVLAKA SAEVTVPYAD RPLDGIFTIA TELSPMTSP TFEVNRPTET EVLLSRLLEK TIRRSGALDT ESLCLVAGQK CWSIRVDVHV MSHDGNLVDA ACIAVVAALR H FRKPDTSI ESGVLTIYTP AEREPVPLSW LHTPFCVTWS FFGDEGEIAV LDATWLEEQV RVGSCTISMN KHGEICQIAK LG GTPVEAV SLLQCTSIAL TKVKEFSDLV DKKLAEDFKR RNPGGLLKEL KAENDR

UniProtKB: Uncharacterized protein

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Macromolecule #2: Exoribonuclease phosphorolytic domain-containing protein

MacromoleculeName: Exoribonuclease phosphorolytic domain-containing protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 29.986879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPLDTSTYKL ALLRVDGRRW NELRRVHAQI RTQAAADGSS YLEMGHTKVM CVVTGPSEPG PRRGTGAGTT GGGGAGGAGG GGSGGQGKE AEVVVSIVIA GFSSVDRKRH GRNDKRIIEM QSTVANALSA SLHTHLFPHS QITISLHVLS QDGSLLAALI N AATLACVD ...String:
MPLDTSTYKL ALLRVDGRRW NELRRVHAQI RTQAAADGSS YLEMGHTKVM CVVTGPSEPG PRRGTGAGTT GGGGAGGAGG GGSGGQGKE AEVVVSIVIA GFSSVDRKRH GRNDKRIIEM QSTVANALSA SLHTHLFPHS QITISLHVLS QDGSLLAALI N AATLACVD AGIPMTDYVV ACTAGSTSTY AANDENADPL LDLNHQEEQE LPWLTVATLG ESDKVAVLVC ESRVQVSRLE GM LAVGVDG CKQIRAILDH VVRQKGRRMI REGAVEKGVS LDDMDED

UniProtKB: Uncharacterized protein

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Macromolecule #3: Exoribonuclease-like protein

MacromoleculeName: Exoribonuclease-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 39.553035 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATDAASAPH SLTFPRGIFA KLSPHPYLLR TLCPDPSNSS STPQRTNGRR PNEARPFRVN LGSLSHAHGS ALVRAGDTTV LCGVRGEVL PVERIPLFRQ PDVNGSGIGA TVGRGELKEY DLLVPNIELA TGSAPQFLPG VPPTALAQTL STRVYSLLHS T RLVSAEEL ...String:
MATDAASAPH SLTFPRGIFA KLSPHPYLLR TLCPDPSNSS STPQRTNGRR PNEARPFRVN LGSLSHAHGS ALVRAGDTTV LCGVRGEVL PVERIPLFRQ PDVNGSGIGA TVGRGELKEY DLLVPNIELA TGSAPQFLPG VPPTALAQTL STRVYSLLHS T RLVSAEEL RIWYRPVATN RSKEGEDVEM EEECQEESGE EQDRVVAYWV LYIDLVFLSF DGNPFDVAWA AVVAALRDTK LP VARWDPD REMVVCSKTE TMKLTIKGLP IACSAAVFLE KEHGEVAVGE KNRHWILLDP DRLEESLCKE VITMVVDFSD GET RIRAIE KQGGTVFGRE LIRSFALVAE DRWKVVKEVM K

UniProtKB: Ribosomal RNA-processing protein 43

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Macromolecule #4: Exoribonuclease phosphorolytic domain-containing protein

MacromoleculeName: Exoribonuclease phosphorolytic domain-containing protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 27.979668 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTTTATTAP EAALGVLPRA DGSARYSHAG YTVTASVNGP IEAQRRDEHP YEAHVDVIVR PAAGVGGTRE RHLESILQSS FAQIILVKS FPRSLIQIVL QVEESPENEY VNTKLVQASL NFAVMPALFQ TAMLALLSAG VPMRATATAT AIALASENGA T KTLIDPSP ...String:
MTTTTATTAP EAALGVLPRA DGSARYSHAG YTVTASVNGP IEAQRRDEHP YEAHVDVIVR PAAGVGGTRE RHLESILQSS FAQIILVKS FPRSLIQIVL QVEESPENEY VNTKLVQASL NFAVMPALFQ TAMLALLSAG VPMRATATAT AIALASENGA T KTLIDPSP RQVELAQSVH VFAFTSQDEL LLAESEGDFT IKEWDAAYET AKNICCRPSP TMDGVQMMAI DDDRLVGPDL RH FIRSTME AKVATDLHWK S

UniProtKB: Exoribonuclease phosphorolytic domain-containing protein

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Macromolecule #5: Exoribonuclease phosphorolytic domain-containing protein

MacromoleculeName: Exoribonuclease phosphorolytic domain-containing protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 43.949383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAASSQHVL LSPAELAYLH ASLSLTPPIR PDGRSPTQFR PLIAETGILP GANGSARVCF ADGTEAIVGV KAEVEKTVSR SKEDEEVGL LVASAGDMDV DDEEGYAKVG ADNRTGEASW VEITVEIPGV RDDDSGMVFL AQLLGEALLA DGEFVKKLWI N RRYHWKLY ...String:
MSAASSQHVL LSPAELAYLH ASLSLTPPIR PDGRSPTQFR PLIAETGILP GANGSARVCF ADGTEAIVGV KAEVEKTVSR SKEDEEVGL LVASAGDMDV DDEEGYAKVG ADNRTGEASW VEITVEIPGV RDDDSGMVFL AQLLGEALLA DGEFVKKLWI N RRYHWKLY IDILLISPPL SYPLPLLSLT THLALLSTRL PRLKSEGDED PYFDDDWAVA PYLFPRSSSA SKSSKSSPTQ PT TRPPITL LVMAVGNNIL FDPSKEELAV ADVALAVSVT ATDVDPDESD AQKETATATA GPDSADAAKR GRKLRLLSIR TID PPSRLT PPGVPNSTNP AAIYGTTSSS GTNGNGQPQQ KVESGKISEP IEPIEGVWRA PRGGAKRLVL GALVQKVLEK GGVV DEVLD ALEGVELT

UniProtKB: Ribosomal RNA-processing protein 42

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Macromolecule #6: Exosome complex component MTR3

MacromoleculeName: Exosome complex component MTR3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 30.541703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDRRRINGP AGATIPPVYE DSGISEVKAL KIRSRPSNII RKIYLKTGVT PSASGSAYLE LETSANSGVS GLKLSCTVHG PRSLPRSSP FSPHMVVSTH VKYAPFATKQ RRGYLRDPTE RDLGIHLEAA LRGAIIADRW PKSGVDIIIS IIEGDQDREA S KTQGDEVW ...String:
MTDRRRINGP AGATIPPVYE DSGISEVKAL KIRSRPSNII RKIYLKTGVT PSASGSAYLE LETSANSGVS GLKLSCTVHG PRSLPRSSP FSPHMVVSTH VKYAPFATKQ RRGYLRDPTE RDLGIHLEAA LRGAIIADRW PKSGVDIIIS IIEGDQDREA S KTQGDEVW DMMNTLSGCI TVASAALADA GIDCVDTVAG GVAALVQDSD GSPEIVVDPI PSEHRKILAA CCVAYLPMRD EV TNLWFRG DLPASDMDLY TELVEKGIQA SRSANRVLVD CLTETVG

UniProtKB: Exosome complex component MTR3

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Macromolecule #7: Ribosomal RNA-processing protein 40

MacromoleculeName: Ribosomal RNA-processing protein 40 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 27.955145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSTTTRPFVL PGETIDPSLV PTHPKHPLRL GPGLRHVPPS DIIPTVAGQL ITNLNKNSMW VEYNSQRYVP TQNDLVLAQV LRSTQDSYL CLITPHTPPA TLPHLAFESA TKKTRPQLQP GQLVYARVSL ANRHMDPELE CVNPSTGKAD GLGPITGPGC V FEVSLGFA ...String:
MSTTTRPFVL PGETIDPSLV PTHPKHPLRL GPGLRHVPPS DIIPTVAGQL ITNLNKNSMW VEYNSQRYVP TQNDLVLAQV LRSTQDSYL CLITPHTPPA TLPHLAFESA TKKTRPQLQP GQLVYARVSL ANRHMDPELE CVNPSTGKAD GLGPITGPGC V FEVSLGFA RRLLMAKSRE EGKVGVLEML AGEDPSIGEA GAGLAFETAV GRNGRVWVGS EDVKTVIIVG RALQETDRGN LT IEGQRKL VRRLLREMR

UniProtKB: Ribosomal RNA-processing protein 40

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Macromolecule #8: Putative exosome complex protein

MacromoleculeName: Putative exosome complex protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 38.403348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPITIHAPLP PPRLHDEDSD VDMSSDSDSS SEGGVPLTSN LPSRAKPKSS LFTTTKSSSD IVTPGELITT SPQFMRGHGT YIPPGTTSI ISSVAGTILR TNKLLSVRPL RARYTPEVGD LVVGRIIEVQ ARRWRVDVGS TQFASLPLSA INLPGGILRK R TETDELQM ...String:
MPITIHAPLP PPRLHDEDSD VDMSSDSDSS SEGGVPLTSN LPSRAKPKSS LFTTTKSSSD IVTPGELITT SPQFMRGHGT YIPPGTTSI ISSVAGTILR TNKLLSVRPL RARYTPEVGD LVVGRIIEVQ ARRWRVDVGS TQFASLPLSA INLPGGILRK R TETDELQM RSFFSEGDLL VAEVQGVYGD GGAVLHTRSL KYGKLRNGVF VAVSGMGGGG GVVRSRRQVW TLEGANGAGL ID VVLGVNG YVWIAKHTED GPGEDPNAST KQVGITNLEE GMSANMYSSQ NDRIEAETMR EIARLRGVVM ALVENGLRVD EDM VMRGYR EAVEMALVSP EGPEDVYLGG ERGRQLAAAL TA

UniProtKB: Putative exosome complex protein

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Macromolecule #9: Putative exosome 3'->5 protein

MacromoleculeName: Putative exosome 3'->5 protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 23.886416 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTTQPTLAL PGQLLGPISK YQPGPGTHVH ESNLYSSLLG TVHVTQPARA PGPVKRLNRI TPAPTPAELP TISVSAARPA GSAASGLVT GRKREILPEV GNIVLCRVIR ITPRQAVVTI LVCGDTVLDA EWQGLIRVQD IRATEKDRVK VYESFRPGDI V RAEVISLG ...String:
MTTTQPTLAL PGQLLGPISK YQPGPGTHVH ESNLYSSLLG TVHVTQPARA PGPVKRLNRI TPAPTPAELP TISVSAARPA GSAASGLVT GRKREILPEV GNIVLCRVIR ITPRQAVVTI LVCGDTVLDA EWQGLIRVQD IRATEKDRVK VYESFRPGDI V RAEVISLG DQANYYLSTA RNELGVILAT SEAGNTMYPV SWREYRDPIT GLTELRKVAK PY

UniProtKB: Putative exosome 3'->5 protein

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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

Concentration0.53 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
4.0 mMNaH2PO4Sodium phosphate (monobasic)
16.0 mMNa2HPO4Sodium phosphate (dibasic)
300.0 mMNaClSodium chloride
1.0 mMC4H10O2S2Dithiothreitol

Details: 20 mM Na-Phosphate buffer pH 7.5, 300 mM NaCl, 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 200 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Details: Grids were glow discharged twice at 15 mA, 0.39 mBar, for 100 seconds each time
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Sample volume 3 ul Wait time 5 s, Blot time 5 s, Delay time 0 s Force 12.
DetailsSample frozen directly after S200 size exclusion column

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6579 / Average exposure time: 6.5 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2448810
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated in RELION from 1541277 particles after 2D classes selection
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 276958
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.1)
Details: Separated particles with missing subunits in cap or barrel
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: Modeller, initial_model_type: in silico modelmulti-template models built using structures of homolog proteins
source_name: AlphaFold, initial_model_type: in silico model

3-f1

RefinementSpace: REAL
Output model

PDB-8r1o:
Structure of C. thermophilum RNA exosome core

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