[English] 日本語
Yorodumi
- EMDB-8444: Structure of bL17-depleted large ribosomal subunit assembly inter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8444
TitleStructure of bL17-depleted large ribosomal subunit assembly intermediate - Class C3
Map dataClass C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate
Sample
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate - Class C3
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsTan Y / Davis JH / Lyumkis D
Funding support United States, Singapore, 7 items
OrganizationGrant numberCountry
Jane Coffin Childs Foundation post-doctoral fellowship United States
Leona M. and Harry B. Helmsley Charitable Trust Grant2012-PG-MED002 United States
National Institute of Aging K99 transitional awardAG050749 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053757 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Agency for Science, Technology and Research Singapore Singapore
Simons Foundation349247 United States
CitationJournal: Cell / Year: 2016
Title: Modular Assembly of the Bacterial Large Ribosomal Subunit.
Authors: Joseph H Davis / Yong Zi Tan / Bridget Carragher / Clinton S Potter / Dmitry Lyumkis / James R Williamson /
Abstract: The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as ...The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway. We find that ribosome biogenesis is a parallel process, that blocks of structured rRNA and proteins assemble cooperatively, and that the entire process is dynamic and can be "re-routed" through different pathways as needed. This work reveals the complex landscape of ribosome assembly in vivo and provides the requisite tools to characterize additional assembly pathways for ribosomes and other macromolecular machines.
History
DepositionOct 25, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseDec 14, 2016-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0263
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0263
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8444.png

Downloads & links

-
Map

FileDownload / File: emd_8444.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 320 pix.
= 419.2 Å		1.31 Å/pix.
x 320 pix.
= 419.2 Å		1.31 Å/pix.
x 320 pix.
= 419.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0263 / Movie #1: 0.0263
Minimum - Maximum-0.046187446 - 0.14411108
Average (Standard dev.)-0.0013047989 (±0.006453684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 419.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z419.200419.200419.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0460.144-0.001

-
Supplemental data

-
Mask #1

Fileemd_8444_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Class C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate -...

Fileemd_8444_additional.map
AnnotationClass C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate - Unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Class C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate -...

Fileemd_8444_half_map_1.map
AnnotationClass C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate - Halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Class C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate -...

Fileemd_8444_half_map_2.map
AnnotationClass C3 bL17-Depleted 50S Ribosomal Biogenesis Intermediate - Halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : bL17-depleted large ribosomal subunit assembly intermediate - Class C3

EntireName: bL17-depleted large ribosomal subunit assembly intermediate - Class C3
Components
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate - Class C3

-
Supramolecule #1: bL17-depleted large ribosomal subunit assembly intermediate - Class C3

SupramoleculeName: bL17-depleted large ribosomal subunit assembly intermediate - Class C3
type: complex / ID: 1 / Parent: 0
Details: E. coli large ribosome subunit purified from bL17-depleted cells.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCM3722 rplQ::cat, pHSL-rplQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris Hydrochloride
100.0 mMNH4ClAmmonium Chloride
10.0 mMMgCl2Magnesium Chloride
0.5 mMC10H16N2O8Ethylenediaminetetraacetic Acid
6.0 mMC2H6OSBeta-mercaptoethanol

Details: Most of the sucrose was removed by spin concentration
GridModel: C-Flat CF-1.2/1.3-4Au / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: 3 microliter of the sample was added..
DetailsFraction was obtained directly from a sucrose gradient, and was spin-concentrated in a 100 kDa MW-cutoff filter.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsIn order to account for highly preferred orientation of the specimen, data was acquired using tilts ranging from 10-60 degrees, in addition to untilted images at 0 degrees. The CTF was estimated on a per-particle basis to account for the gradient of CTF values across individual micrographs
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number grids imaged: 2 / Number real images: 2479 / Average exposure time: 10.0 sec. / Average electron dose: 34.27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 38167 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
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: 447017
Details: 84028 particles were initially picked with DoG picker. These particles were put through 2D classification. Good class 2D class averages then served as templates for FindEM. FindEM picked a ...Details: 84028 particles were initially picked with DoG picker. These particles were put through 2D classification. Good class 2D class averages then served as templates for FindEM. FindEM picked a total of 447017 particles.
CTF correctionSoftware: (Name: CTFFIND (ver. 3), CTFTILT, Gctf (ver. 0.5), Appion)
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model was produced from the 2D class averages using Optimod in the Appion pipeline.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.07) / Number images used: 12394
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.07)
Final 3D classificationNumber classes: 3 / Avg.num./class: 8700 / Software - Name: FREALIGN (ver. 9.07)
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