[English] 日本語
Yorodumi
- EMDB-57776: Structure of the 70S ribosome with E- and P-site tRNA from the al... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-57776
TitleStructure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi.
Map dataStationary phase Asaia platycodi ribosome bound to E- and P-site tRNA.
Sample
  • Complex: Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi
KeywordsRibosome / 70S / P-site tRNA / E-site tRNA
Biological speciesAsaia platycodi JCM 25414 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsChan LI / Omae K / Amikura K / Suzuki S / Melnikov SM
Funding support United Kingdom, Japan, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008695/1 United Kingdom
Royal SocietyICA/R2/242249 United Kingdom
Japan Science and TechnologyJPMJCR20S4 Japan
CitationJournal: To Be Published
Title: Hibernation factors are prone to structural divergence and spontaneous loss in bacterial species
Authors: Chan LI / Melnikov SV
History
DepositionApr 27, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_57776.png

Downloads & links

-
Map

FileDownload / File: emd_57776.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStationary phase Asaia platycodi ribosome bound to E- and P-site tRNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-0.51104236 - 1.0144053
Average (Standard dev.)0.0028028889 (±0.049135007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A for "Stationary phase Asaia platycodi...

Fileemd_57776_half_map_1.map
AnnotationHalf map A for "Stationary phase Asaia platycodi ribosome bound to E- and P-site tRNA".
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B for "Stationary phase Asaia platycodi...

Fileemd_57776_half_map_2.map
AnnotationHalf map B for "Stationary phase Asaia platycodi ribosome bound to E- and P-site tRNA".
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of the 70S ribosome with E- and P-site tRNA from the al...

EntireName: Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi
Components
  • Complex: Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi

-
Supramolecule #1: Structure of the 70S ribosome with E- and P-site tRNA from the al...

SupramoleculeName: Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.642 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris hydrochloride
20.0 mMMg(CH3COO)2Magnesium acetate
50.0 mMKClPotassium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.2)
Software - details: cryoSPARC was used to process cryo-EM data
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.2)
Software - details: cryoSPARC was used to process cryo-EM data
Number images used: 22155
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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