[English] 日本語
Yorodumi
- EMDB-5907: Cryo-EM structure of low salt treated immature 30S ribosomal subu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5907
TitleCryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
Map datathe map is normalized to N(0,1)
Sample
  • Sample: Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
  • Complex: low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
Keywords30S subunit assembly / RsgA / RbfA / 17S rRNA processing
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.3 Å
AuthorsYang Z / Guo Q / Goto S / Chen Y / Li N / Yan K / Zhang Y / Muto A / Deng H / Himeno H ...Yang Z / Guo Q / Goto S / Chen Y / Li N / Yan K / Zhang Y / Muto A / Deng H / Himeno H / Lei J / Gao N
CitationJournal: Protein Cell / Year: 2014
Title: Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence.
Authors: Zhixiu Yang / Qiang Guo / Simon Goto / Yuling Chen / Ningning Li / Kaige Yan / Yixiao Zhang / Akira Muto / Haiteng Deng / Hyouta Himeno / Jianlin Lei / Ning Gao /
Abstract: The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA ...The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.
History
DepositionFeb 12, 2014-
Header (metadata) releaseMar 12, 2014-
Map releaseApr 9, 2014-
UpdateJun 11, 2014-
Current statusJun 11, 2014Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5907.gif

Downloads & links

-
Map

FileDownload / File: emd_5907.map.gz / Format: CCP4 / Size: 7.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe map is normalized to N(0,1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3 Å/pix.
x 124 pix.
= 372. Å		3 Å/pix.
x 124 pix.
= 372. Å		3 Å/pix.
x 124 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.12 / Movie #1: 3.12
Minimum - Maximum-3.6619153 - 14.59147072
Average (Standard dev.)0.0 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-61-61-61
Dimensions124124124
Spacing124124124
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z124124124
origin x/y/z0.0000.0000.000
length x/y/z372.000372.000372.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-61-61-61
NC/NR/NS124124124
D min/max/mean-3.66214.591-0.000

-
Supplemental data

-
Sample components

-
Entire : Cryo-EM structure of low salt treated immature 30S ribosomal subu...

EntireName: Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
Components
  • Sample: Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
  • Complex: low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain

-
Supramolecule #1000: Cryo-EM structure of low salt treated immature 30S ribosomal subu...

SupramoleculeName: Cryo-EM structure of low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

-
Supramolecule #1: low salt treated immature 30S ribosomal subunit from rsga and rbf...

SupramoleculeName: low salt treated immature 30S ribosomal subunit from rsga and rbfa deleted E.coli strain
type: complex / ID: 1 / Name.synonym: immature 30S / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: SSU 30S
Source (natural)Organism: Escherichia coli (E. coli) / Strain: A19
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 20mM Tris-HCl, 150mM NH4Cl,10mM Mg(OAc)2
StainingType: NEGATIVE / Details: grids were prepared with an FEI Vitrobot Mark IV
GridDetails: Quantifoil 2/4 grids were coated with carbon and glow discharged in a Harrick Plasma Cleaner for 30 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: blot for 1 second before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJul 14, 2012
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 4365 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Detailsthis is a classification volume (NO.5 of five groups) using RELION
CTF correctionDetails: weiner filter
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.3 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 37804

+
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