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- EMDB-1438: Architecture of the yeast Rrp44 exosome complex suggests routes o... -

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Basic information

Entry
Database: EMDB / ID: EMD-1438
TitleArchitecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.
Map dataThis is the map of yeast Rrp44-associated exosome complex
Sample
  • Sample: Rrp44-associated exosome complex
  • Protein or peptide: Rrp44
  • Protein or peptide: Rrp43
  • Protein or peptide: Rrp4
  • Protein or peptide: Csl4
  • Protein or peptide: Rrp45
  • Protein or peptide: Rrp46-TAP
  • Protein or peptide: Rrp41
  • Protein or peptide: Rrp42
  • Protein or peptide: Mtr3
  • Protein or peptide: Rrp40
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å
AuthorsWang H-W / Wang J / Ding F / Callahan K / Bratkowski MA / Butler JS / Nogales E / Ke A
CitationJournal: Proc Natl Acad Sci U S A / Year: 2007
Title: Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.
Authors: Hong-Wei Wang / Jianjun Wang / Fang Ding / Kevin Callahan / Matthew A Bratkowski / J Scott Butler / Eva Nogales / Ailong Ke /
Abstract: The eukaryotic core exosome (CE) is a conserved nine-subunit protein complex important for 3' end trimming and degradation of RNA. In yeast, the Rrp44 protein constitutively associates with the CE ...The eukaryotic core exosome (CE) is a conserved nine-subunit protein complex important for 3' end trimming and degradation of RNA. In yeast, the Rrp44 protein constitutively associates with the CE and provides the sole source of processive 3'-to-5' exoribonuclease activity. Here we present EM reconstructions of the core and Rrp44-bound exosome complexes. The two-lobed Rrp44 protein binds to the RNase PH domain side of the exosome and buttresses the bottom of the exosome-processing chamber. The Rrp44 C-terminal body part containing an RNase II-type active site is anchored to the exosome through a conserved set of interactions mainly to the Rrp45 and Rrp43 subunit, whereas the Rrp44 N-terminal head part is anchored to the Rrp41 subunit and may function as a roadblock to restrict access of RNA to the active site in the body region. The Rrp44-exosome (RE) architecture suggests an active site sequestration mechanism for strict control of 3' exoribonuclease activity in the RE complex.
History
DepositionOct 3, 2007-
Header (metadata) releaseOct 3, 2007-
Map releaseOct 3, 2007-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.080558
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6.080558
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1438.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of yeast Rrp44-associated exosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.18 Å/pix.
x 72 pix.
= 372.96 Å
5.18 Å/pix.
x 72 pix.
= 372.96 Å
5.18 Å/pix.
x 72 pix.
= 372.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.18 Å
Density
Contour Level1: 1.5 / Movie #1: 6.080558
Minimum - Maximum-3.07122 - 15.728899999999999
Average (Standard dev.)0.00000000205625 (±0.999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 372.96 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.185.185.18
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z372.960372.960372.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-3.07115.7290.000

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Supplemental data

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Sample components

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Entire : Rrp44-associated exosome complex

EntireName: Rrp44-associated exosome complex
Components
  • Sample: Rrp44-associated exosome complex
  • Protein or peptide: Rrp44
  • Protein or peptide: Rrp43
  • Protein or peptide: Rrp4
  • Protein or peptide: Csl4
  • Protein or peptide: Rrp45
  • Protein or peptide: Rrp46-TAP
  • Protein or peptide: Rrp41
  • Protein or peptide: Rrp42
  • Protein or peptide: Mtr3
  • Protein or peptide: Rrp40

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Supramolecule #1000: Rrp44-associated exosome complex

SupramoleculeName: Rrp44-associated exosome complex / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 10
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa

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Macromolecule #1: Rrp44

MacromoleculeName: Rrp44 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 110 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #2: Rrp43

MacromoleculeName: Rrp43 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 40 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #3: Rrp4

MacromoleculeName: Rrp4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 40 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #4: Csl4

MacromoleculeName: Csl4 / type: protein_or_peptide / ID: 4 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #5: Rrp45

MacromoleculeName: Rrp45 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #6: Rrp46-TAP

MacromoleculeName: Rrp46-TAP / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #7: Rrp41

MacromoleculeName: Rrp41 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa

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Macromolecule #8: Rrp42

MacromoleculeName: Rrp42 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #9: Mtr3

MacromoleculeName: Mtr3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #10: Rrp40

MacromoleculeName: Rrp40 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Molecular weightExperimental: 30 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.04 mg/mL
BufferpH: 7.5
Details: 25mM Tris-HCl, 50 mM NaCl, 2 mM DTT, and 10 uM ZnCl2
StainingType: NEGATIVE
Details: Four microliters of the protein solution was negatively stained with 2% uranyl formate solution between two thin layers of carbon on a copper grid by using the sandwich method
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 49000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 6.6 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 49000
Sample stageSpecimen holder: normal single-tilt holder / Specimen holder model: OTHER / Tilt angle max: 55
TemperatureAverage: 300 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at
DetailsLow dose mode for taking pictures
DateAug 1, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.7 µm / Number real images: 50 / Average electron dose: 20 e/Å2 / Details: The scanner was Nikon Super Coolscan 8000 / Od range: 1.4 / Bits/pixel: 14
Tilt angle min0

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Image processing

Final two d classificationNumber classes: 50
Final angle assignmentDetails: SPIDER: theta 90 degrees, phi 90 degrees
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER
Details: Final map were calculated from all the untilted particles
Number images used: 3020

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Atomic model buiding 1

SoftwareName: Situs
DetailsProtocol: Rigid Body. 2NN6.pdb and 2IX0.pdb were used to dock in the map. The latter one was separated to three domains after the automatic docking and manually adjusted to fit in the map locally in Chimera.
RefinementProtocol: RIGID BODY FIT

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