[English] 日本語
Yorodumi
- EMDB-41264: DIV 1 hippocampal neuron (weighted back-projection and greyscale ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41264
TitleDIV 1 hippocampal neuron (weighted back-projection and greyscale segmentation)
Map data
Sample
  • Cell: DIV 1 Hippocampal Neuron
Keywordshippocampus / neuron / tomography / segmentation / STRUCTURAL PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodelectron tomography / cryo EM
AuthorsSwulius MT
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To be Published
Title: Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models.
Authors: Purnell C / Heebner J / Hylton RH / Kabonick S / Grillo M / Grigoryev S / Heberle F / Waxham NM / Swulius MT
History
DepositionJul 16, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41264.png

Downloads & links

-
Map

FileDownload / File: emd_41264.map.gz / Format: CCP4 / Size: 141.9 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 13.6 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)34.465359999999997 (±7.426957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14391024101
Spacing10241439101
CellA: 13926.4 Å / B: 19570.4 Å / C: 1373.6001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_41264_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DIV 1 Hippocampal Neuron

EntireName: DIV 1 Hippocampal Neuron
Components
  • Cell: DIV 1 Hippocampal Neuron

-
Supramolecule #1: DIV 1 Hippocampal Neuron

SupramoleculeName: DIV 1 Hippocampal Neuron / type: cell / ID: 1 / Parent: 0
Details: Weighted Back-projection and Greyscale Segmentation
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 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 defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 60

+
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