[English] 日本語
Yorodumi
- EMDB-27809: 3D Reconstruction of PPG Matrix-Landed GroEL Protein Complexes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27809
Title3D Reconstruction of PPG Matrix-Landed GroEL Protein Complexes
Map data3D Reconstruction of PPG Matrix-Landed GroEL Protein Complexes
Sample
  • Complex: Chaperonin 60
KeywordsMatrix-Landed / CHAPERONE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsSalome AZ / Westphall MS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118110 United States
CitationJournal: To Be Published
Title: Matrix-Landing Mass Spectrometry for Electron Microscopy Imaging of Native Protein Complexes
Authors: Salome AZ / Westphall MS
History
DepositionAug 8, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27809.png

Downloads & links

-
Map

FileDownload / File: emd_27809.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D Reconstruction of PPG Matrix-Landed GroEL Protein Complexes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 128 pix.
= 435.2 Å		3.4 Å/pix.
x 128 pix.
= 435.2 Å		3.4 Å/pix.
x 128 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.173
Minimum - Maximum-0.1326944 - 0.42658857
Average (Standard dev.)-0.012079393 (±0.0328936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Chaperonin 60

EntireName: Chaperonin 60
Components
  • Complex: Chaperonin 60

-
Supramolecule #1: Chaperonin 60

SupramoleculeName: Chaperonin 60 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
DetailsProtein complex solution was ionized and converted to gas-phase via electrospray ionization. GroEL gas-phase ions were collected for analysis.

-
Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: OTHER / Average electron dose: 100.0 e/Å2 / Details: NanoSprint15 MK-II 15 Mpix camera (AMT Imaging)
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

-
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: cisTEM / Number images used: 20922
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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