[English] 日本語
Yorodumi
- EMDB-62303: Structure of Alpha-hemolysin heptameric pore state derived from E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62303
TitleStructure of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes.
Map dataMap of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes.
Sample
  • Complex: Heptameric pore complex of alpha-hemolysin from the Egg-PC/SM derived liposomes
KeywordsPore-forming toxin (PFT) / Alpha hemolysin / Liposome / TOXIN
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChatterjee A / Roy A / Dutta S
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST-FIST (SR/FST/LSII-039/2015) India
Department of Biotechnology (DBT, India)(BT/INF/22/SP22844/2017) India
CitationJournal: To Be Published
Title: Structure of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes
Authors: Chatterjee A / Roy A / Dutta S
History
DepositionNov 7, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62303.png

Downloads & links

-
Map

FileDownload / File: emd_62303.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 280 pix.
= 257.6 Å		0.92 Å/pix.
x 280 pix.
= 257.6 Å		0.92 Å/pix.
x 280 pix.
= 257.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.48845735 - 0.8322823
Average (Standard dev.)0.00013168615 (±0.025422372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 257.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half-map of Alpha-hemolysin heptameric pore state derived from...

Fileemd_62303_half_map_1.map
AnnotationHalf-map of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map of Alpha-hemolysin heptameric pore state derived from...

Fileemd_62303_half_map_2.map
AnnotationHalf-map of Alpha-hemolysin heptameric pore state derived from Egg-PC/SM liposomes.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heptameric pore complex of alpha-hemolysin from the Egg-PC/SM der...

EntireName: Heptameric pore complex of alpha-hemolysin from the Egg-PC/SM derived liposomes
Components
  • Complex: Heptameric pore complex of alpha-hemolysin from the Egg-PC/SM derived liposomes

-
Supramolecule #1: Heptameric pore complex of alpha-hemolysin from the Egg-PC/SM der...

SupramoleculeName: Heptameric pore complex of alpha-hemolysin from the Egg-PC/SM derived liposomes
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 330 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180700
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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