[English] 日本語
Yorodumi
- EMDB-0481: Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0481
TitleRole of Era in Assembly and Homeostasis of the Ribosomal Small Subunit
Map data30S subunit assembly intermediate (class D) obtained by depleting Era in E. coli
Sample
  • Complex: 30S assembly intermediate (class D)
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsRazi A / Davis JH / Hao Y / Jahagirdar D / Thurlow B / Basu K / Jain N / Gomez-Blanco J / Britton RA / Vargas J ...Razi A / Davis JH / Hao Y / Jahagirdar D / Thurlow B / Basu K / Jain N / Gomez-Blanco J / Britton RA / Vargas J / Guarne A / Woodson SA / Williamson JR / Ortega J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health ResearchPJT-153044 Canada
CitationJournal: Nucleic Acids Res / Year: 2019
Title: Role of Era in assembly and homeostasis of the ribosomal small subunit.
Authors: Aida Razi / Joseph H Davis / Yumeng Hao / Dushyant Jahagirdar / Brett Thurlow / Kaustuv Basu / Nikhil Jain / Josue Gomez-Blanco / Robert A Britton / Javier Vargas / Alba Guarné / Sarah A ...Authors: Aida Razi / Joseph H Davis / Yumeng Hao / Dushyant Jahagirdar / Brett Thurlow / Kaustuv Basu / Nikhil Jain / Josue Gomez-Blanco / Robert A Britton / Javier Vargas / Alba Guarné / Sarah A Woodson / James R Williamson / Joaquin Ortega /
Abstract: Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is ...Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era's role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.
History
DepositionJan 20, 2019-
Header (metadata) releaseJan 30, 2019-
Map releaseJun 26, 2019-
UpdateSep 25, 2019-
Current statusSep 25, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 6.31
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0481.png

Downloads & links

-
Map

FileDownload / File: emd_0481.map.gz / Format: CCP4 / Size: 13.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S subunit assembly intermediate (class D) obtained by depleting Era in E. coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.15 Å/pix.
x 152 pix.
= 326.192 Å		2.15 Å/pix.
x 152 pix.
= 326.192 Å		2.15 Å/pix.
x 152 pix.
= 326.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.146 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.31 / Movie #1: 6.31
Minimum - Maximum-20.061335 - 38.385986000000003
Average (Standard dev.)0.15835243 (±1.5023782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions152152152
Spacing152152152
CellA=B=C: 326.192 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1462.1462.146
M x/y/z152152152
origin x/y/z0.0000.0000.000
length x/y/z326.192326.192326.192
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS152152152
D min/max/mean-20.06138.3860.158

-
Supplemental data

-
Sample components

-
Entire : 30S assembly intermediate (class D)

EntireName: 30S assembly intermediate (class D)
Components
  • Complex: 30S assembly intermediate (class D)

-
Supramolecule #1: 30S assembly intermediate (class D)

SupramoleculeName: 30S assembly intermediate (class D) / type: complex / ID: 1 / Parent: 0
Details: 30S assembly intermediate (class D) purified from Era-depleted E.coli cells
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 900 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Details: 5 mAmps Glow discharge before sample was applied to the grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 25 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 847135
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2avy
PDB Unreleased entry

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0.) / Number images used: 186369
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1.0.)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1.0.)
Final 3D classificationSoftware - Name: RELION (ver. 2.1.0.)
FSC plot (resolution estimation)

+
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