[English] 日本語
Yorodumi
- EMDB-2612: Incomplete pneumolysin oligomers form membrane pores -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2612
TitleIncomplete pneumolysin oligomers form membrane pores
Map dataSub-tomogram average of 197 pre-pores.
Sample
  • Sample: Pneumolysin prepore formed on a cholesterol-containing liposome
  • Organelle or cellular component: synthetic membrane
  • Protein or peptide: pneumolysin
Keywordscholesterol-dependent cytolysin / pneumolysin / proteolipid toroidal pore
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin
Similarity search - Domain/homology
Biological speciessynthetic construct (others) / Streptococcus pneumoniae (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsSonnen AF-P / Plitzko JM / Gilbert RJC
CitationJournal: Open Biol / Year: 2014
Title: Incomplete pneumolysin oligomers form membrane pores.
Authors: Andreas F-P Sonnen / Jürgen M Plitzko / Robert J C Gilbert /
Abstract: Pneumolysin is a member of the cholesterol-dependent cytolysin (CDC) family of pore-forming proteins that are produced as water-soluble monomers or dimers, bind to target membranes and oligomerize ...Pneumolysin is a member of the cholesterol-dependent cytolysin (CDC) family of pore-forming proteins that are produced as water-soluble monomers or dimers, bind to target membranes and oligomerize into large ring-shaped assemblies comprising approximately 40 subunits and approximately 30 nm across. This pre-pore assembly then refolds to punch a large hole in the lipid bilayer. However, in addition to forming large pores, pneumolysin and other CDCs form smaller lesions characterized by low electrical conductance. Owing to the observation of arc-like (rather than full-ring) oligomers by electron microscopy, it has been hypothesized that smaller oligomers explain smaller functional pores. To investigate whether this is the case, we performed cryo-electron tomography of pneumolysin oligomers on model lipid membranes. We then used sub-tomogram classification and averaging to determine representative membrane-bound low-resolution structures and identified pre-pores versus pores by the presence of membrane within the oligomeric curve. We found pre-pore and pore forms of both complete (ring) and incomplete (arc) oligomers and conclude that arc-shaped oligomeric assemblies of pneumolysin can form pores. As the CDCs are evolutionarily related to the membrane attack complex/perforin family of proteins, which also form variably sized pores, our findings are of relevance to that class of proteins as well.
History
DepositionMar 25, 2014-
Header (metadata) releaseApr 9, 2014-
Map releaseMay 7, 2014-
UpdateMay 7, 2014-
Current statusMay 7, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 10.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2612.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of 197 pre-pores.
Voxel sizeX=Y=Z: 4.72 Å
Density
Contour LevelBy AUTHOR: 10.699999999999999 / Movie #1: 10.7
Minimum - Maximum-47.705104830000003 - 66.461158749999996
Average (Standard dev.)1.89449048 (±8.68987179)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions104104104
Spacing104104104
CellA=B=C: 490.87997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.724.724.72
M x/y/z104104104
origin x/y/z0.0000.0000.000
length x/y/z490.880490.880490.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS104104104
D min/max/mean-47.70566.4611.894

-
Supplemental data

-
Sample components

-
Entire : Pneumolysin prepore formed on a cholesterol-containing liposome

EntireName: Pneumolysin prepore formed on a cholesterol-containing liposome
Components
  • Sample: Pneumolysin prepore formed on a cholesterol-containing liposome
  • Organelle or cellular component: synthetic membrane
  • Protein or peptide: pneumolysin

-
Supramolecule #1000: Pneumolysin prepore formed on a cholesterol-containing liposome

SupramoleculeName: Pneumolysin prepore formed on a cholesterol-containing liposome
type: sample / ID: 1000 / Oligomeric state: Full ring oligomer / Number unique components: 2
Molecular weightTheoretical: 2 MDa

-
Supramolecule #1: synthetic membrane

SupramoleculeName: synthetic membrane / type: organelle_or_cellular_component / ID: 1
Details: Liposome formed of a 10:10:1 mixture of phosphatidylcholine:cholesterol:dicetyl phosphate
Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: pneumolysin

MacromoleculeName: pneumolysin / type: protein_or_peptide / ID: 1
Details: pneumolysin added to the synthetic membranes spontaneously forms oligomers on their surfaces.
Oligomeric state: 40mer / Recombinant expression: Yes
Source (natural)Organism: Streptococcus pneumoniae (bacteria) / Location in cell: cytoplasm
Molecular weightExperimental: 52 KDa / Theoretical: 52 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: M15 / Recombinant plasmid: pKK233-2
SequenceUniProtKB: Pneumolysin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: PBS
GridDetails: C-flat or lacy carbon-coated grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 64171
Specialist opticsEnergy filter - Name: GIF2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °
DateJun 1, 2008
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: OTHER / Software - Name: TOM, Toolbox, Bsoft, XMIPP / Number subtomograms used: 197
DetailsSubtomograms were selected manually in Bshow and subjected to automatic maximum-likelihood based classification using XMIPP.

+
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