[English] 日本語
Yorodumi
- EMDB-24633: E. coli bL17-limitation ribosome assembly intermediate #5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24633
TitleE. coli bL17-limitation ribosome assembly intermediate #5
Map dataE. coli bL17-limitation ribosome assembly intermediate #5 (D-class)
Sample
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate #5
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsRabuck-Gibbons JN / Lyumkis D / Williamson JR
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP5-OD021396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 AI150472 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM136412 United States
CitationJournal: Structure / Year: 2022
Title: Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates.
Authors: Jessica N Rabuck-Gibbons / Dmitry Lyumkis / James R Williamson /
Abstract: Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations ...Single-particle cryoelectron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct particle populations into different groups through computational classification. However, there is a dearth of tools for surveying the heterogeneity landscape, quantitatively analyzing heterogeneous particle populations after classification, deciding how many unique classes are represented by the data, and accurately cross-comparing reconstructions. Here, we develop a workflow that contains discovery and analysis modules to quantitatively mine cryo-EM data for sets of structures with maximal diversity. This workflow was applied to a dataset of E. coli 50S ribosome assembly intermediates, which are characterized by significant structural heterogeneity. We identified more detailed branchpoints in the assembly process and characterized the interactions of an assembly factor with immature intermediates. While the tools described here were developed for ribosome assembly, they should be broadly applicable to the analysis of other heterogeneous cryo-EM datasets.
History
DepositionAug 6, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 5.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24633.png

Downloads & links

-
Map

FileDownload / File: emd_24633.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli bL17-limitation ribosome assembly intermediate #5 (D-class)
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: 5.6 / Movie #1: 5.6
Minimum - Maximum-5.017995 - 14.810351
Average (Standard dev.)-0.42552108 (±1.0477182)
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/NZ000
NX/NY/NZ448448448
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-5.01814.810-0.426

-
Supplemental data

-
Additional map: E. coli bL17-limitation ribosome assembly intermediate #5 (D-class)...

Fileemd_24633_additional_1.map
AnnotationE. coli bL17-limitation ribosome assembly intermediate #5 (D-class) unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: E. coli bL17-limitation ribosome assembly intermediate #5 (D-class)...

Fileemd_24633_additional_2.map
AnnotationE. coli bL17-limitation ribosome assembly intermediate #5 (D-class) binarized map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: E. coli bL17-limitation ribosome assembly intermediate #5 (D-class)...

Fileemd_24633_additional_3.map
AnnotationE. coli bL17-limitation ribosome assembly intermediate #5 (D-class) binned, unmasked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: E. coli bL17-limitation ribosome assembly intermediate #5 (D-class)...

Fileemd_24633_half_map_1.map
AnnotationE. coli bL17-limitation ribosome assembly intermediate #5 (D-class) odd halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: E. coli bL17-limitation ribosome assembly intermediate #5 (D-class)...

Fileemd_24633_half_map_2.map
AnnotationE. coli bL17-limitation ribosome assembly intermediate #5 (D-class) even halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : bL17-depleted large ribosomal subunit assembly intermediate #5

EntireName: bL17-depleted large ribosomal subunit assembly intermediate #5
Components
  • Complex: bL17-depleted large ribosomal subunit assembly intermediate #5

-
Supramolecule #1: bL17-depleted large ribosomal subunit assembly intermediate #5

SupramoleculeName: bL17-depleted large ribosomal subunit assembly intermediate #5
type: complex / ID: 1 / Parent: 0
Details: bL17-depleted large ribosomal subunit assembly intermediate #5
Source (natural)Organism: Escherichia coli (E. coli) / Strain: NCM3722
Molecular weightTheoretical: 1.5 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormula
20.0 mMTrisHCl
100.0 mMNH4Cl
10.0 mMMgCl2
0.5 mMEDTA
6.0 mMb-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: 3 ul of this sample was added to 3 plasma cleaned (Gatan, Solarus) 1.2mm hole, 1.3mm spacing holey gold grids (Russo and Passmore, 2014). Grids were manually frozen in liquid ethane..
Detailsdepleted ribosome assembly intermediate purified by sucrose gradient

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsIn order to account for highly preferred orientation of the specimen, data was acquired using a tilt of -20 degrees.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 833 / Average exposure time: 10.0 sec. / Average electron dose: 35.0 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 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

CTF correctionSoftware - Name: CTFFIND
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. X) / Number images used: 3243
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN (ver. X) / Details: FrealignX
Final 3D classificationSoftware - Name: FREALIGN (ver. X)
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