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- EMDB-51133: 80S-bound human Ski2-exosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51133
Title80S-bound human Ski2-exosome complex
Map data
Sample
  • Complex: 80S-bound human Ski2-exosome complex
    • Protein or peptide: x 12 types
    • RNA: x 1 types
KeywordsRibosome / RNase / Helicase / RNA-binding / mRNA-degradation / cytoplasm
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II activity / exoribonuclease II / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / Ski complex ...DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II activity / exoribonuclease II / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / Ski complex / CUT catabolic process / exosome (RNase complex) / U4 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of isotype switching / 3'-5' RNA helicase activity / nuclear mRNA surveillance / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / ribosome disassembly / RNA catabolic process / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / mRNA catabolic process / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / translation elongation factor activity / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / cytosolic ribosome / rescue of stalled ribosome / euchromatin / fibrillar center / rRNA processing / chromosome / positive regulation of cell growth / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / ciliary basal body / immune response / RNA helicase / translation / GTPase activity / intracellular membrane-bounded organelle / centrosome / GTP binding / nucleolus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / Exosome complex exonuclease RRP44, S1 domain / S1 domain ...Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / Exosome complex exonuclease RRP44, S1 domain / S1 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 / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / : / Ribonuclease II/R, conserved site / rRNA-processing arch domain / Ribonuclease II family signature. / Mtr4-like, beta-barrel domain / : / Ribonuclease II/R / RNB domain / RNB / : / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / : / GTP-eEF1A C-terminal domain-like / 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 / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / 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 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Superkiller complex protein 2 / Exosome complex component MTR3 / DIS3-like exonuclease 1 / Exosome complex component RRP43 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 ...Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Superkiller complex protein 2 / Exosome complex component MTR3 / DIS3-like exonuclease 1 / Exosome complex component RRP43 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex component CSL4 / HBS1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Cricket paralysis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKoegel A / Keidel A / Loukeri MJ / Kuhn CC / Langer LM / Schaefer IB / Conti E
Funding support Germany, European Union, Denmark, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)740329European Union
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
CitationJournal: Nature / Year: 2024
Title: Structural basis of mRNA decay by the human exosome-ribosome supercomplex.
Authors: Alexander Kögel / Achim Keidel / Matina-Jasemi Loukeri / Christopher C Kuhn / Lukas M Langer / Ingmar B Schäfer / Elena Conti /
Abstract: The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated ...The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largely by the cytoplasmic exosome, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. ). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex.
History
DepositionJul 23, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51133.png

Downloads & links

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Map

FileDownload / File: emd_51133.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 832 pix.
= 708.198 Å		0.85 Å/pix.
x 832 pix.
= 708.198 Å		0.85 Å/pix.
x 832 pix.
= 708.198 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.015523653 - 0.038076628
Average (Standard dev.)0.000021217098 (±0.0005251272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions832832832
Spacing832832832
CellA=B=C: 708.19836 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51133_msk_1.map
Projections & Slices
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Half map: halfA

Fileemd_51133_half_map_1.map
AnnotationhalfA
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Half map: halfB

Fileemd_51133_half_map_2.map
AnnotationhalfB
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Sample components

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Entire : 80S-bound human Ski2-exosome complex

EntireName: 80S-bound human Ski2-exosome complex
Components
  • Complex: 80S-bound human Ski2-exosome complex
    • Protein or peptide: Exosome complex component RRP41
    • Protein or peptide: Exosome complex component RRP43
    • Protein or peptide: Exosome complex component RRP46
    • Protein or peptide: Exosome complex component RRP42
    • Protein or peptide: Exosome complex component RRP40
    • Protein or peptide: Exosome complex component CSL4
    • RNA: CrPV-IRES RNA
    • Protein or peptide: Helicase SKI2W
    • Protein or peptide: Exosome complex component MTR3
    • Protein or peptide: Exosome complex component RRP4
    • Protein or peptide: Isoform 2 of HBS1-like protein
    • Protein or peptide: Exosome complex component RRP45
    • Protein or peptide: DIS3-like exonuclease 1

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Supramolecule #1: 80S-bound human Ski2-exosome complex

SupramoleculeName: 80S-bound human Ski2-exosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Exosome complex component RRP41

MacromoleculeName: Exosome complex component RRP41 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.416996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA VVYGPHEIRG SRARALPDRA LVNCQYSSAT FSTGERKRR PHGDRKSCEM GLQLRQTFEA AILTQLHPRS QIDIYVQVLQ ADGGTYAACV NAATLAVLDA GIPMRDFVCA C SAGFVDGT ...String:
MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA VVYGPHEIRG SRARALPDRA LVNCQYSSAT FSTGERKRR PHGDRKSCEM GLQLRQTFEA AILTQLHPRS QIDIYVQVLQ ADGGTYAACV NAATLAVLDA GIPMRDFVCA C SAGFVDGT ALADLSHVEE AAGGPQLALA LLPASGQIAL LEMDARLHED HLERVLEAAA QAARDVHTLL DRVVRQHVRE AS ILLGD

UniProtKB: Exosome complex component RRP41

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Macromolecule #2: Exosome complex component RRP43

MacromoleculeName: Exosome complex component RRP43 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.429893 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAAGFK TVEPLEYYRR FLKENCRPDG RELGEFRTTT VNIGSISTAD GSALVKLGNT TVICGVKAEF AAPSTDAPDK GYVVPNVDL PPLCSSRFRS GPPGEEAQVA SQFIADVIEN SQIIQKEDLC ISPGKLVWVL YCDLICLDYD GNILDACTFA L LAALKNVQ ...String:
GPDSMAAGFK TVEPLEYYRR FLKENCRPDG RELGEFRTTT VNIGSISTAD GSALVKLGNT TVICGVKAEF AAPSTDAPDK GYVVPNVDL PPLCSSRFRS GPPGEEAQVA SQFIADVIEN SQIIQKEDLC ISPGKLVWVL YCDLICLDYD GNILDACTFA L LAALKNVQ LPEVTINEET ALAEVNLKKK SYLNIRTHPV ATSFAVFDDT LLIVDPTGEE EHLATGTLTI VMDEEGKLCC LH KPGGSGL TGAKLQDCMS RAVTRHKEVK KLMDEVIKSM KPK

UniProtKB: Exosome complex component RRP43

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Macromolecule #3: Exosome complex component RRP46

MacromoleculeName: Exosome complex component RRP46 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.636312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMEEETH TDAKIRAENG TGSSPRGPGC SLRHFACEQN LLSRPDGSAS FLQGDTSVLA GVYGPAEVKV SKEIFNKATL EVILRPKIG LPGVAEKSRE RLIRNTCEAV VLGTLHPRTS ITVVLQVVSD AGSLLACCLN AACMALVDAG VPMRALFCGV A CALDSDGT ...String:
GPDSMEEETH TDAKIRAENG TGSSPRGPGC SLRHFACEQN LLSRPDGSAS FLQGDTSVLA GVYGPAEVKV SKEIFNKATL EVILRPKIG LPGVAEKSRE RLIRNTCEAV VLGTLHPRTS ITVVLQVVSD AGSLLACCLN AACMALVDAG VPMRALFCGV A CALDSDGT LVLDPTSKQE KEARAVLTFA LDSVERKLLM SSTKGLYSDT ELQQCLAAAQ AASQHVFRFY RESLQRRYSK S

UniProtKB: Exosome complex component RRP46

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Macromolecule #4: Exosome complex component RRP42

MacromoleculeName: Exosome complex component RRP42 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.216762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMASVTL SEAEKVYIVH GVQEDLRVDG RGCEDYRCVE VETDVVSNTS GSARVKLGHT DILVGVKAEM GTPKLEKPNE GYLEFFVDC SASATPEFEG RGGDDLGTEI ANTLYRIFNN KSSVDLKTLC ISPREHCWVL YVDVLLLECG GNLFDAISIA V KAALFNTR ...String:
GPDSMASVTL SEAEKVYIVH GVQEDLRVDG RGCEDYRCVE VETDVVSNTS GSARVKLGHT DILVGVKAEM GTPKLEKPNE GYLEFFVDC SASATPEFEG RGGDDLGTEI ANTLYRIFNN KSSVDLKTLC ISPREHCWVL YVDVLLLECG GNLFDAISIA V KAALFNTR IPRVRVLEDE EGSKDIELSD DPYDCIRLSV ENVPCIVTLC KIGYRHVVDA TLQEEACSLA SLLVSVTSKG VV TCMRKVG KGSLDPESIF EMMETGKRVG KVLHASLQSV VHKEESLGPK RQKVGFLG

UniProtKB: Exosome complex component RRP42

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Macromolecule #5: Exosome complex component RRP40

MacromoleculeName: Exosome complex component RRP40 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.940502 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAEPAS VAAESLAGSR ARAARTVLGQ VVLPGEELLL PEQEDAEGPG GAVERPLSLN ARACSRVRVV CGPGLRRCGD RLLVTKCGR LRHKEPGSGS GGGVYWVDSQ QKRYVPVKGD HVIGIVTAKS GDIFKVDVGG SEPASLSYLS FEGATKRNRP N VQVGDLIY ...String:
GPDSMAEPAS VAAESLAGSR ARAARTVLGQ VVLPGEELLL PEQEDAEGPG GAVERPLSLN ARACSRVRVV CGPGLRRCGD RLLVTKCGR LRHKEPGSGS GGGVYWVDSQ QKRYVPVKGD HVIGIVTAKS GDIFKVDVGG SEPASLSYLS FEGATKRNRP N VQVGDLIY GQFVVANKDM EPEMVCIDSC GRANGMGVIG QDGLLFKVTL GLIRKLLAPD CEIIQEVGKL HPLEIVFGMN GR IWVKAKT IQQTLILANI LEACEHMTSD QRKQIFSRLA ES

UniProtKB: Exosome complex component RRP40

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Macromolecule #6: Exosome complex component CSL4

MacromoleculeName: Exosome complex component CSL4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.8351 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAPPVR YCIPGERLCN LEEGSPGSGT YTRHGYIFSS LAGCLMKSSE NGALPVVSVV RETESQLLPD VGAIVTCKVS SINSRFAKV HILYVGSMPL KNSFRGTIRK EDVRATEKDK VEIYKSFRPG DIVLAKVISL GDAQSNYLLT TAENELGVVV A HSESGIQM ...String:
GPDSMAPPVR YCIPGERLCN LEEGSPGSGT YTRHGYIFSS LAGCLMKSSE NGALPVVSVV RETESQLLPD VGAIVTCKVS SINSRFAKV HILYVGSMPL KNSFRGTIRK EDVRATEKDK VEIYKSFRPG DIVLAKVISL GDAQSNYLLT TAENELGVVV A HSESGIQM VPISWCEMQC PKTHTKEFRK VARVQPEFLQ T

UniProtKB: Exosome complex component CSL4

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Macromolecule #8: Helicase SKI2W

MacromoleculeName: Helicase SKI2W / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.913688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ LFLSSPAWLP LHGVEHSARK WQRKTDPWS LLAVLGAPVP SDLQAQRHPT TGQILGYKEV LLENTNLSAT TSLSLRRPPG PASQSLWGNP TQYPFWPGGM D EPTITDLN ...String:
MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ LFLSSPAWLP LHGVEHSARK WQRKTDPWS LLAVLGAPVP SDLQAQRHPT TGQILGYKEV LLENTNLSAT TSLSLRRPPG PASQSLWGNP TQYPFWPGGM D EPTITDLN TREEAEEEID FEKDLLTIPP GFKKGMDFAP KDCPTPAPGL LSLSCMLEPL DLGGGDEDEN EAVGQPGGPR GD TVSASPC SAPLARASSL EDLVLKEAST AVSTPEAPEP PSQEQWAIPV DATSPVGDFY RLIPQPAFQW AFEPDVFQKQ AIL HLERHD SVFVAAHTSA GKTVVAEYAI ALAQKHMTRT IYTSPIKALS NQKFRDFRNT FGDVGLLTGD VQLHPEASCL IMTT EILRS MLYSGSDVIR DLEWVIFDEV HYINDVERGV VWEEVLIMLP DHVSIILLSA TVPNALEFAD WIGRLKRRQI YVIST VTRP VPLEHYLFTG NSSKTQGELF LLLDSRGAFH TKGYYAAVEA KKERMSKHAQ TFGAKQPTHQ GGPAQDRGVY LSLLAS LRT RAQLPVVVFT FSRGRCDEQA SGLTSLDLTT SSEKSEIHLF LQRCLARLRG SDRQLPQVLH MSELLNRGLG VHHSGIL PI LKEIVEMLFS RGLVKVLFAT ETFAMGVNMP ARTVVFDSMR KHDGSTFRDL LPGEYVQMAG RAGRRGLDPT GTVILLCK G RVPEMADLHR MMMGKPSQLQ SQFRLTYTMI LNLLRVDALR VEDMMKRSFS EFPSRKDSKA HEQALAELTK RLGALEEPD MTGQLVDLPE YYSWGEELTE TQHMIQRRIM ESVNGLKSLS AGRVVVVKNQ EHHNALGVIL QVSSNSTSRV FTTLVLCDKP LSQDPQDRG PATAEVPYPD DLVGFKLFLP EGPCDHTVVK LQPGDMAAIT TKVLRVNGEK ILEDFSKRQQ PKFKKDPPLA A VTTAVQEL LRLAQAHPAG PPTLDPVNDL QLKDMSVVEG GLRARKLEEL IQGAQCVHSP RFPAQYLKLR ERMQIQKEME RL RFLLSDQ SLLLLPEYHQ RVEVLRTLGY VDEAGTVKLA GRVACAMSSH ELLLTELMFD NALSTLRPEE IAALLSGLVC QSP GDAGDQ LPNTLKQGIE RVRAVAKRIG EVQVACGLNQ TVEEFVGELN FGLVEVVYEW ARGMPFSELA GLSGTPEGLV VRCI QRLAE MCRSLRGAAR LVGEPVLGAK METAATLLRR DIVFAASLYT Q

UniProtKB: Superkiller complex protein 2

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Macromolecule #9: Exosome complex component MTR3

MacromoleculeName: Exosome complex component MTR3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.267127 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAP AALRGRLLCD FRRAPFAGRR RRAPPGGCEE RELALALQEA LEPAVRLGRY PRAQLEVSAL LLEDGGSALA A ALTAAALA ...String:
MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAP AALRGRLLCD FRRAPFAGRR RRAPPGGCEE RELALALQEA LEPAVRLGRY PRAQLEVSAL LLEDGGSALA A ALTAAALA LADAGVEMYD LVVGCGLSLA PGPAPTWLLD PTRLEEERAA AGLTVALMPV LNQVAGLLGS GEGGLTESWA EA VRLGLEG CQRLYPVLQQ SLVRAARRRG AAAQP

UniProtKB: Exosome complex component MTR3

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Macromolecule #10: Exosome complex component RRP4

MacromoleculeName: Exosome complex component RRP4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.190355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMAMEMR LPVARKPLSE RLGRDTKKHL VVPGDTITTD TGFMRGHGTY MGEEKLIASV AGSVERVNKL ICVKALKTRY IGEVGDIVV GRITEVQQKR WKVETNSRLD SVLLLSSMNL PGGELRRRSA EDELAMRGFL QEGDLISAEV QAVFSDGAVS L HTRSLKYG ...String:
GPDSMAMEMR LPVARKPLSE RLGRDTKKHL VVPGDTITTD TGFMRGHGTY MGEEKLIASV AGSVERVNKL ICVKALKTRY IGEVGDIVV GRITEVQQKR WKVETNSRLD SVLLLSSMNL PGGELRRRSA EDELAMRGFL QEGDLISAEV QAVFSDGAVS L HTRSLKYG KLGQGVLVQV SPSLVKRQKT HFHDLPCGAS VILGNNGFIW IYPTPEHKEE EAGGFIANLE PVSLADREVI SR LRNCIIS LVTQRMMLYD TSILYCYEAS LPHQIKDILK PEIMEEIVME TRQRLLEQEG

UniProtKB: Exosome complex component RRP4

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Macromolecule #11: Isoform 2 of HBS1-like protein

MacromoleculeName: Isoform 2 of HBS1-like protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.196131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSSQCESP SLTELFQEHK ENNISQCFTL SDLCNQSSAS FTDLSLGSFP LSQLANRCQS SPGISELTGS LSSLAFHKAS PTRDLENLS LSELIAETID VDNSQIKKES FEVSLSEVRS PGIDSNIDLS VLIKNPDFVP KPVVDPSIAP SSRTKVLSSK L GKNSNFAK ...String:
GPDSSQCESP SLTELFQEHK ENNISQCFTL SDLCNQSSAS FTDLSLGSFP LSQLANRCQS SPGISELTGS LSSLAFHKAS PTRDLENLS LSELIAETID VDNSQIKKES FEVSLSEVRS PGIDSNIDLS VLIKNPDFVP KPVVDPSIAP SSRTKVLSSK L GKNSNFAK DNKKNNKGSL TRKPPFSLSW TKALAARPSA FASTLCLRYP LKSCKRRTLD LYKTFLYSRQ VQDVKDKEIS PL VAITPFD FKSASPDDIV KANQKKAFTR ELEVLFQ

UniProtKB: HBS1-like protein

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Macromolecule #12: Exosome complex component RRP45

MacromoleculeName: Exosome complex component RRP45 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.370312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMKETPL SNCERRFLLR AIEEKKRLDG RQTYDYRNIR ISFGTDYGCC IVELGKTRVL GQVSCELVSP KLNRATEGIL FFNLELSQM AAPAFEPGRQ SDLLVKLNRL MERCLRNSKC IDTESLCVVA GEKVWQIRVD LHLLNHDGNI IDAASIAAIV A LCHFRRPD ...String:
GPDSMKETPL SNCERRFLLR AIEEKKRLDG RQTYDYRNIR ISFGTDYGCC IVELGKTRVL GQVSCELVSP KLNRATEGIL FFNLELSQM AAPAFEPGRQ SDLLVKLNRL MERCLRNSKC IDTESLCVVA GEKVWQIRVD LHLLNHDGNI IDAASIAAIV A LCHFRRPD VSVQGDEVTL YTPEERDPVP LSIHHMPICV SFAFFQQGTY LLVDPNEREE RVMDGLLVIA MNKHREICTI QS SGGIMLL KDQVLRCSKI AGVKVAEITE LILKALENDQ KVRKEGGKFG FAESIANQRI TAFKMEKAPI DTSDVEEKAE EII AEAEPP SEVVSTPVLW TPGTAQIGEG VENSWGDLED SEKEDDEGGG DQAIILDGIK MDTGVEVSDI GSQDAPIILS DSEE EEMII LEPDKNPKKI RTQTTSAKQE KAPSKKPVKR RKKKRAAN

UniProtKB: Exosome complex component RRP45

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Macromolecule #13: DIS3-like exonuclease 1

MacromoleculeName: DIS3-like exonuclease 1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: exoribonuclease II
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 121.108555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMLQKREKV LLLRTFQGRT LRIVREHYLR PCVPCHSPLC PQPAACSHDG KLLSSDVTHY VIPDWKVVQD YLEILEFPEL KGIIFMQTA CQAVQHQRGR RQYNKLRNLL KDARHDCILF ANEFQQCCYL PRERGESMEK WQTRSIYNAA VWYYHHCQDR M PIVMVTED ...String:
GPMLQKREKV LLLRTFQGRT LRIVREHYLR PCVPCHSPLC PQPAACSHDG KLLSSDVTHY VIPDWKVVQD YLEILEFPEL KGIIFMQTA CQAVQHQRGR RQYNKLRNLL KDARHDCILF ANEFQQCCYL PRERGESMEK WQTRSIYNAA VWYYHHCQDR M PIVMVTED EEAIQQYGSE TEGVFVITFK NYLDNFWPDL KAAHELCDSI LQSRRERENE SQESHGKEYP EHLPLEVLEA GI KSGRYIQ GILNVNKHRA QIEAFVRLQG ASSKDSDLVS DILIHGMKAR NRSIHGDVVV VELLPKNEWK GRTVALCEND CDD KASGES PSEPMPTGRV VGILQKNWRD YVVTFPSKEE VQSQGKNAQK ILVTPWDYRI PKIRISTQQA ETLQDFRVVV RIDS WESTS VYPNGHFVRV LGRIGDLEGE IATILVENSI SVIPFSEAQM CEMPVNTPES PWKVSPEEEQ KRKDLRKSHL VFSID PKGC EDVNDTLSVR TLNNGNLELG VHIADVTHFV APNSYIDIEA RTRATTYYLA DRRYDMLPSV LSADLCSLLG GVDRYA VSI MWELDKASYE IKKVWYGRTI IRSAYKLFYE AAQELLDGNL SVVDDIPEFK DLDEKSRQAK LEELVWAIGK LTDIARH VR AKRDGCGALE LEGVEVCVQL DDKKNIHDLI PKQPLEVHET VAECMILANH WVAKKIWESF PHQALLRQHP PPHQEFFS E LRECAKAKGF FIDTRSNKTL ADSLDNANDP HDPIVNRLLR SMATQAMSNA LYFSTGSCAE EEFHHYGLAL DKYTHFTSP IRRYSDIVVH RLLMAAISKD KKMEIKGNLF SNKDLEELCR HINNRNQAAQ HSQKQSTELF QCMYFKDKDP ATEERCISDG VIYSIRTNG VLLFIPRFGI KGAAYLKNKD GLVISCGPDS CSEWKPGSLQ RFQNKITSTT TDGESVTFHL FDHVTVRISI Q ASRCHSDT IRLEIISNKP YKIPNTELIH QSSPLLKSEL VKEVTKSVEE AQLAQEVKVN IIQEEYQEYR QTKGRSLYTL LE EIRDLAL LDVSNNYGI

UniProtKB: DIS3-like exonuclease 1

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Macromolecule #7: CrPV-IRES RNA

MacromoleculeName: CrPV-IRES RNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Cricket paralysis virus
Molecular weightTheoretical: 13.422399 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUCUCC UCUUUUUUUU UUUU

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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
GridModel: Quantifoil R2/1 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6d6q

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79353
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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