[English] 日本語
Yorodumi
- EMDB-1439: Architecture of the yeast Rrp44 exosome complex suggests routes o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1439
TitleArchitecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.
Map dataThis is the 3D map of yeast exosome core complex
Sample
  • Sample: exosome core complex
  • Protein or peptide: Rrp43
  • Protein or peptide: Rrp4
  • Protein or peptide: Cls4
  • 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: 23.0 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 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
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

1439.gif

Downloads & links

-
Map

FileDownload / File: emd_1439.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the 3D map of yeast exosome core 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

Histogram

Histogram (log scale)
Contour Level1: 2.0 / Movie #1: 6.080558
Minimum - Maximum-4.22665 - 19.953499999999998
Average (Standard dev.)-0.0000000035545 (±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-4.22719.953-0.000

-
Supplemental data

-
Sample components

+
Entire : exosome core complex

EntireName: exosome core complex
Components
  • Sample: exosome core complex
  • Protein or peptide: Rrp43
  • Protein or peptide: Rrp4
  • Protein or peptide: Cls4
  • 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

+
Supramolecule #1000: exosome core complex

SupramoleculeName: exosome core complex / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 9
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa

+
Macromolecule #1: Rrp43

MacromoleculeName: Rrp43 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: bakers' yeast
Molecular weightExperimental: 50 KDa

+
Macromolecule #2: Rrp4

MacromoleculeName: Rrp4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 40 KDa

+
Macromolecule #3: Cls4

MacromoleculeName: Cls4 / type: protein_or_peptide / ID: 3 / Details: substoichiometric during purification / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightExperimental: 40 KDa

+
Macromolecule #4: Rrp45

MacromoleculeName: Rrp45 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 40 KDa

+
Macromolecule #5: Rrp46-TAP

MacromoleculeName: Rrp46-TAP / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightExperimental: 40 KDa

+
Macromolecule #6: Rrp41

MacromoleculeName: Rrp41 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa

+
Macromolecule #7: Rrp42

MacromoleculeName: Rrp42 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa

+
Macromolecule #8: Mtr3

MacromoleculeName: Mtr3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa

+
Macromolecule #9: Rrp40

MacromoleculeName: Rrp40 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 30 KDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.5
Details: 25 mM 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

-
Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureAverage: 300 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DetailsLow dose mode was used 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 micrographs were scanned on a Nikon Super Coolscan 8000 scanner
Od range: 1.4 / Bits/pixel: 14
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 49000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: Final map were calculated from all the particles. / Number images used: 2980
Final angle assignmentDetails: SPIDER: theta 90 degrees, phi 90 degrees
Final two d classificationNumber classes: 50

-
Atomic model buiding 1

Initial modelPDB ID:

2nn6

SoftwareName: Situs
DetailsProtocol: Rigid Body. The docking was performed by automatic rigid body docking in Situs.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more