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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


CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / RNA processing / rRNA processing / nucleolus / RNA binding / 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 / Exosome complex component RRP45 / 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
Citation
Journal: Nat Commun / Year: 2025
Title: 4D structural biology-quantitative dynamics in the eukaryotic RNA exosome complex.
Authors: Jobst Liebau / Daniela Lazzaretti / Torben Fürtges / Anna Bichler / Michael Pilsl / Till Rudack / Remco Sprangers /
Abstract: Molecular machines play pivotal roles in all biological processes. Most structural methods, however, are unable to directly probe molecular motions. Here, we demonstrate that dedicated NMR ...Molecular machines play pivotal roles in all biological processes. Most structural methods, however, are unable to directly probe molecular motions. Here, we demonstrate that dedicated NMR experiments can provide quantitative insights into functionally important dynamic regions in very large asymmetric protein complexes. We establish this for the 410 kDa eukaryotic RNA exosome complex that contains ten distinct protein chains. Methyl-group and fluorine NMR experiments reveal site-specific interactions among subunits and with an RNA substrate. Furthermore, we extract quantitative insights into conformational changes within the complex in response to substrate and subunit binding for regions that are invisible in static cryo-EM and crystal structures. In particular, we identify a flexible plug region that can block an aberrant route for RNA towards the active site. Based on molecular dynamics simulations and NMR data, we provide a model that shows how the flexible plug is structured in the open and closed conformations. Our work thus demonstrates that a combination of state-of-the-art structural biology methods can provide quantitative insights into large molecular machines that go significantly beyond the well-resolved and static images of biomolecular complexes, thereby adding the time domain to structural biology.
#1: Journal: 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-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing 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
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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

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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

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18825_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18825_half_map_2.map
Projections & Slices
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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: Exosome complex component RRP45

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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
CTF correctionSoftware: (Name: RELION (ver. 4.0.1), CTFFIND (ver. 4.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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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