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- EMDB-0127: Human nuclear RNA exosome EXO-14 complex -

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Basic information

Entry
Database: EMDB / ID: 0127
TitleHuman nuclear RNA exosome EXO-14 complex
Map dataCryo-EM reconstruction of the human nuclear RNA exosome EXO-14 complex
SampleHuman nuclear RNA exosome EXO-14 complex:
EXOSC9 / EXOSC4 / EXOSC8 / EXOSC5 / EXOSC7 / EXOSC6 / EXOSC3 / EXOSC2 / EXOSC1 / DIS3 ...EXOSC9 / EXOSC4 / EXOSC8 / EXOSC5 / EXOSC7 / EXOSC6 / EXOSC3 / EXOSC2 / EXOSC1 / DIS3 / MPP6 / EXOSC10 / C1D / MTR4 / nucleic-acidNucleic acid
Sourcesynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 6.25 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.
DateDeposition: Jul 12, 2018 / Header (metadata) release: Jul 25, 2018 / Map release: Aug 1, 2018 / Last update: Aug 8, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • 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_0127.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:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.066417865 - 0.118277155
Average (Standard dev.)0.00018988713 (0.0038044313)
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-0.0660.1180.000

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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: 18

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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, Human nuclear RNA exosome EXO-14 complex

ProteinName: Human nuclear RNA exosome EXO-14 complex / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Human nuclear RNA exosome EXO-14 complex

ProteinName: Human nuclear RNA exosome EXO-14 complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, EXOSC9

ProteinName: EXOSC9 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, EXOSC4

ProteinName: EXOSC4 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, EXOSC8

ProteinName: EXOSC8 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, EXOSC5

ProteinName: EXOSC5 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, EXOSC7

ProteinName: EXOSC7 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, EXOSC6

ProteinName: EXOSC6 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, EXOSC3

ProteinName: EXOSC3 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, EXOSC2

ProteinName: EXOSC2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, EXOSC1

ProteinName: EXOSC1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, DIS3

ProteinName: DIS3 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, MPP6

ProteinName: MPP6 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: protein, EXOSC10

ProteinName: EXOSC10 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #16: protein, C1D

ProteinName: C1D / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #17: protein, MTR4

ProteinName: MTR4 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #18: nucleic-acid, U44 ssRNA

Nucleic-acidName: U44 ssRNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU
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: 13804
3D reconstructionResolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF

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