[English] 日本語
Yorodumi
- EMDB-82120: In Situ Subtomogram Average of the 80S Ribosome in the Soma of Ra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-82120
TitleIn Situ Subtomogram Average of the 80S Ribosome in the Soma of Rat Hippocampal Neurons
Map data
Sample
  • Cell: Primary cultured rat hippocampal neurons
    • Complex: 60S large ribosomal subunit
    • Complex: 40S small ribosomal subunit
Keywords80S Ribosome / Somatic ribosome / Protein synthesis / In situ / RIBOSOME
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsXia YN / Yan YT / Si Z / Wu J / Gu ML / Tian CL / Lu ZH / Liu S / Huang WL / Tang PP ...Xia YN / Yan YT / Si Z / Wu J / Gu ML / Tian CL / Lu ZH / Liu S / Huang WL / Tang PP / Rong CYL / Liu YT / Zhou ZH / Zhang XK / Wang PY / Lau PM / Bi GQ / Tao CL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Compartment-specific organization and activity-dependent remodeling of ribosomes in hippocampal synapses
Authors: Xia YN / Yan YT / Si Z / Wu J / Gu ML / Tian CL / Lu ZH / Liu S / Huang WL / Tang PP / Rong CYL / Liu YT / Zhou ZH / Zhang XK / Wang PY / Lau PM / Bi GQ / Tao CL
History
DepositionJul 15, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_82120.png

Downloads & links

-
Map

FileDownload / File: emd_82120.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.69 Å/pix.
x 256 pix.
= 689.664 Å		2.69 Å/pix.
x 256 pix.
= 689.664 Å		2.69 Å/pix.
x 256 pix.
= 689.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.694 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.233
Minimum - Maximum-0.29284802 - 0.54656607
Average (Standard dev.)0.0032482187 (±0.049722124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 689.664 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_82120_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_82120_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_82120_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Primary cultured rat hippocampal neurons

EntireName: Primary cultured rat hippocampal neurons
Components
  • Cell: Primary cultured rat hippocampal neurons
    • Complex: 60S large ribosomal subunit
    • Complex: 40S small ribosomal subunit

-
Supramolecule #1: Primary cultured rat hippocampal neurons

SupramoleculeName: Primary cultured rat hippocampal neurons / type: cell / ID: 1 / Parent: 0
Details: Primary hippocampal neurons cultured in vitro from Sprague-Dawley (CD(SD) IGS) rats
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley (CD(SD) IGS) / Organ: brain / Tissue: hippocampus

-
Supramolecule #2: 60S large ribosomal subunit

SupramoleculeName: 60S large ribosomal subunit / type: complex / ID: 2 / Parent: 1
Details: Primary hippocampal neurons cultured in vitro from Sprague-Dawley (CD(SD) IGS) rats
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley (CD(SD) IGS) / Organ: brain / Tissue: hippocampus
Molecular weightTheoretical: 2.8 MDa

-
Supramolecule #3: 40S small ribosomal subunit

SupramoleculeName: 40S small ribosomal subunit / type: complex / ID: 3 / Parent: 1
Details: Primary hippocampal neurons cultured in vitro from Sprague-Dawley (CD(SD) IGS) rats
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley (CD(SD) IGS) / Organ: brain / Tissue: hippocampus
Molecular weightTheoretical: 1.5 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 3.7
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
Details: The grids were plasma treated to render the carbon support film hydrophilic before sample application.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 307 K

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 3.66 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: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 3256
ExtractionNumber tomograms: 11 / Number images used: 3492 / Software - Name: RELION (ver. 5.0)
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
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