[English] 日本語
Yorodumi
- EMDB-3153: Cryo-EM structure of the 60S-Arx1-Rei1 complex at near-atomic res... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3153
TitleCryo-EM structure of the 60S-Arx1-Rei1 complex at near-atomic resolution
Map dataCryo-EM reconstruction of the 60S-Arx1-Rei1 complex at near-atomic resolution
Sample
  • Sample: 60S-Arx1-Rei1 complex
  • Complex: 60S ribosomal subunit
  • Protein or peptide: Arx1
  • Protein or peptide: Rei1
Keywordseukaryotic ribosome / 60S subunit / ribosome biogenesis / Rei1 / Arx1 / cytoplasmic maturation
Function / homology
Function and homology information


ribosome biogenesis => GO:0042254 / budding cell bud growth / Hydrolases / nucleocytoplasmic transport / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / Neutrophil degranulation / ribosomal large subunit biogenesis / metallopeptidase activity / mitotic cell cycle ...ribosome biogenesis => GO:0042254 / budding cell bud growth / Hydrolases / nucleocytoplasmic transport / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / Neutrophil degranulation / ribosomal large subunit biogenesis / metallopeptidase activity / mitotic cell cycle / sequence-specific DNA binding / nucleolus / proteolysis / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger protein 622/Rei1/Reh1 / ZN622/Rei1/Reh1, zinc finger C2H2-type / C2H2 type zinc-finger (2 copies) / : / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Creatinase/aminopeptidase-like / zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...Zinc finger protein 622/Rei1/Reh1 / ZN622/Rei1/Reh1, zinc finger C2H2-type / C2H2 type zinc-finger (2 copies) / : / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Creatinase/aminopeptidase-like / zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cytoplasmic 60S subunit biogenesis factor REI1 / Probable metalloprotease ARX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGreber BJ / Gerhardy S / Leitner A / Leibundgut M / Salem M / Boehringer D / Leulliot N / Aebersold R / Panse VG / Ban N
CitationJournal: Cell / Year: 2016
Title: Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.
Authors: Basil Johannes Greber / Stefan Gerhardy / Alexander Leitner / Marc Leibundgut / Michèle Salem / Daniel Boehringer / Nicolas Leulliot / Ruedi Aebersold / Vikram Govind Panse / Nenad Ban /
Abstract: Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, ...Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation.
History
DepositionSep 15, 2015-
Header (metadata) releaseSep 30, 2015-
Map releaseDec 16, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD_3153_500...

Downloads & links

-
Map

FileDownload / File: emd_3153.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the 60S-Arx1-Rei1 complex at near-atomic resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 216 pix.
= 300.24 Å		1.39 Å/pix.
x 216 pix.
= 300.24 Å		1.39 Å/pix.
x 216 pix.
= 300.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.51979357 - 0.87405241
Average (Standard dev.)0.00580786 (±0.05011464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z300.240300.240300.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.5200.8740.006

-
Supplemental data

-
Sample components

-
Entire : 60S-Arx1-Rei1 complex

EntireName: 60S-Arx1-Rei1 complex
Components
  • Sample: 60S-Arx1-Rei1 complex
  • Complex: 60S ribosomal subunit
  • Protein or peptide: Arx1
  • Protein or peptide: Rei1

-
Supramolecule #1000: 60S-Arx1-Rei1 complex

SupramoleculeName: 60S-Arx1-Rei1 complex / type: sample / ID: 1000
Oligomeric state: 1:1:1 stoichiometry of 60S subunit and associated factors
Number unique components: 3
Molecular weightTheoretical: 2.3 MDa

-
Supramolecule #1: 60S ribosomal subunit

SupramoleculeName: 60S ribosomal subunit / type: complex / ID: 1 / Recombinant expression: No
Ribosome-details: ribosome-eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S
Ref GO0: GO:0022625
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Organelle: Cytosol / Location in cell: Cytosol
Molecular weightTheoretical: 2.2 MDa

-
Macromolecule #1: Arx1

MacromoleculeName: Arx1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741 / synonym: Baker's yeast / Organelle: Cytosol and nucleus / Location in cell: Cytosol and nucleus
Molecular weightTheoretical: 65 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: Codon Plus / Recombinant plasmid: pET-47
SequenceUniProtKB: Probable metalloprotease ARX1 / GO: ribosome biogenesis => GO:0042254

-
Macromolecule #2: Rei1

MacromoleculeName: Rei1 / type: protein_or_peptide / ID: 2 / Details: C-terminal His6-tag / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Organelle: Cytosol / Location in cell: Cytosol
Molecular weightTheoretical: 45 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta / Recombinant plasmid: pET-24a
SequenceUniProtKB: Cytoplasmic 60S subunit biogenesis factor REI1 / GO: ribosome biogenesis => GO:0042254

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
Details: 20 mM HEPES-KOH pH 8, 100 mM NaCl, 5 mM MgCl2, 5 mM beta-mercaptoethanol
GridDetails: Quantifoil holey carbon R2/1, glow discharged
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Method: Manual blotting from the back before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsData collected using 4 exposures per ice hole (2 x 2 pattern). Movie mode readout in FEI EPU: 7 frames per exosure
DateJun 13, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1534 / Average electron dose: 20 e/Å2
Details: movie mode readout in FEI EPU: 7 frames per exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100720 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsParticles were selected semi-automatically using BATCHBOXER (EMAN). CTF correction using CTFFIND3. Reconstruction using RELION.
CTF correctionDetails: per micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION1.3 / Details: Particles selected in BATCHBOXER (EMAN1.9). / Number images used: 54775

-
Atomic model buiding 1

Initial modelPDB ID:

4v8t

SoftwareName: UCSF Chimera
DetailsThe coordinate model of the lower-resolution structure of the 60S-Arx1-Rei1 complex was fitted into the cryo-EM density using UCSF CHIMERA. The model was then adjusted using COOT (RNA) and O (proteins).
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