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- EMDB-0128: Human nuclear RNA exosome EXO-10-MPP6 complex -

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Entry
Database: EMDB / ID: 0128
TitleHuman nuclear RNA exosome EXO-10-MPP6 complex
Map dataCryo-EM reconstruction of the human nuclear RNA exosome EXO-10-MPP6 complex
SampleHuman nuclear RNA exosome EXO-14 complex:
exosome complex / U44 ssRNA / (Exosome complex component ...) x 9 / Exosome complex exonuclease RRP44 / M-phase phosphoprotein 6 / nucleic-acidNucleic acid
Function / homologyExosome complex component Rrp43 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 1 / Exosome complex exonuclease RRP44, S1 domain / K Homology domain, type 1 superfamily / Exoribonuclease, PH domain 2 superfamily / Rrp44-like cold shock domain / Exoribonuclease, phosphorolytic domain 1 / PIN domain / K Homology domain, type 1 ...Exosome complex component Rrp43 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 1 / Exosome complex exonuclease RRP44, S1 domain / K Homology domain, type 1 superfamily / Exoribonuclease, PH domain 2 superfamily / Rrp44-like cold shock domain / Exoribonuclease, phosphorolytic domain 1 / PIN domain / K Homology domain, type 1 / Nucleic acid-binding, OB-fold / M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / Exosome complex component CSL4, C-terminal / Ribosomal protein S5 domain 2-type fold / Ribonuclease II/R, conserved site / RNA-binding domain, S1 / Exosome complex component, N-terminal domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / PNPase/RNase PH domain superfamily / PIN-like domain superfamily / Exosome complex component RRP45 / 3' exoribonuclease family, domain 2 / Rrp40, S1 domain / Ribonuclease II family signature. / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / S1 domain / KH domain / Exosome complex exonuclease RRP4 N-terminal region / KSRP (KHSRP) binds and destabilizes mRNA / Rrp44-like cold shock domain / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA decay by 3' to 5' exoribonuclease / PIN domain / ATF4 activates genes / Exosome component EXOSC1/CSL4 / DNA deamination / rRNA 3'-end processing / maturation of 5.8S rRNA / nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription / U1 snRNA 3'-end processing / exosome (RNase complex) / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent tRNA catabolic process / nuclear exosome (RNase complex) / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / CUT catabolic process / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear polyadenylation-dependent rRNA catabolic process / polyadenylation-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / histone mRNA catabolic process / nuclear mRNA surveillance / Endoribonucleases Producing 5'-Phosphomonoesters / exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay / isotype switching / AU-rich element binding / rRNA catabolic process / positive regulation of isotype switching / RNA phosphodiester bond hydrolysis, exonucleolytic / nuclear-transcribed mRNA catabolic process / 7S RNA binding / RNA catabolic process / intermediate filament cytoskeleton / 3'-5'-exoribonuclease activity / Exoribonucleases Producing 5'-Phosphomonoesters / transcriptionally active chromatin / RNA polymerase II activating transcription factor binding / guanyl-nucleotide exchange factor activity / nuclear chromosome / rRNA processing / regulation of mRNA stability / defense response to virus / positive regulation of cell growth / endonuclease activity / immune response / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / membrane / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm / Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Exosome complex component MTR3 / Exosome complex component RRP43 / M-phase phosphoprotein 6 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex exonuclease RRP44 / Exosome complex component CSL4
Function and homology information
SourceHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsGerlach P / Schuller JM / Falk S / Basquin J / Conti E
CitationJournal: Elife / Year: 2018
Title: Distinct and evolutionary conserved structural features of the human nuclear exosome complex.
Authors: Piotr Gerlach / Jan M Schuller / Fabien Bonneau / Jérôme Basquin / Peter Reichelt / Sebastian Falk / Elena Conti
Abstract: The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to ...The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.
Validation ReportPDB-ID: 6h25

SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Aug 15, 2018 / Last update: Aug 15, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6h25
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0128.map.gz (map file in CCP4 format, 62501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.35 Å/pix.
= 337.5 Å
250 pix
1.35 Å/pix.
= 337.5 Å
250 pix
1.35 Å/pix.
= 337.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.24137774 - 0.3664702
Average (Standard dev.)0.00017617023 (0.00808426)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin0.0.0.
Limit249.249.249.
Spacing250250250
CellA=B=C: 337.5 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z337.500337.500337.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.2410.3660.000

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Supplemental data

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Sample components

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Entire Human nuclear RNA exosome EXO-14 complex

EntireName: Human nuclear RNA exosome EXO-14 complex / Number of components: 15

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Component #1: protein, Human nuclear RNA exosome EXO-14 complex

ProteinName: Human nuclear RNA exosome EXO-14 complex / Recombinant expression: No

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Component #2: protein, exosome complex

ProteinName: exosome complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, U44 ssRNA

ProteinName: U44 ssRNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Exosome complex component RRP45

ProteinName: Exosome complex component RRP45 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.370312 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Exosome complex component RRP41

ProteinName: Exosome complex component RRP41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.773328 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Exosome complex component RRP43

ProteinName: Exosome complex component RRP43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.317828 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Exosome complex component RRP46

ProteinName: Exosome complex component RRP46 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.52425 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Exosome complex component RRP42

ProteinName: Exosome complex component RRP42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.216762 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Exosome complex component MTR3

ProteinName: Exosome complex component MTR3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.623469 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, Exosome complex component RRP40

ProteinName: Exosome complex component RRP40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.906359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, Exosome complex component RRP4

ProteinName: Exosome complex component RRP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.190355 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, Exosome complex component CSL4

ProteinName: Exosome complex component CSL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.8351 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, Exosome complex exonuclease RRP44

ProteinName: Exosome complex exonuclease RRP44 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 109.522227 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, M-phase phosphoprotein 6

ProteinName: M-phase phosphoprotein 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.542234 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: nucleic-acid, U44 ssRNA

Nucleic-acidName: U44 ssRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU
MassTheoretical: 13.426333 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 8047

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 110958
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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