[English] 日本語
Yorodumi
- EMDB-8187: aerolysin pore cryo-EM map -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8187
Titleaerolysin pore cryo-EM map
Map dataaerolysin WT pore in LMNG mmicelle
Sample
  • Complex: aerolysin pore
    • Protein or peptide: Aerolysin
Keywordspore forming toxin / concentric beta-barrel / aerolysin / Toxin
Function / homology
Function and homology information


toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Aerolysin / Aerolysin toxin / Aerolysin toxin / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / C-type lectin fold
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsIacovache I / Zuber B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation139098 Switzerland
CitationJournal: Nat Commun / Year: 2016
Title: Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process.
Authors: Ioan Iacovache / Sacha De Carlo / Nuria Cirauqui / Matteo Dal Peraro / F Gisou van der Goot / Benoît Zuber /
Abstract: Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural ...Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural biologists for decades. PFTs are generally secreted as water-soluble monomers and subsequently bind the membrane of target cells. Then, they assemble into circular oligomers, which undergo conformational changes that allow membrane insertion leading to pore formation and potentially cell death. Aerolysin, produced by the human pathogen Aeromonas hydrophila, is the founding member of a major PFT family found throughout all kingdoms of life. We report cryo-electron microscopy structures of three conformational intermediates and of the final aerolysin pore, jointly providing insight into the conformational changes that allow pore formation. Moreover, the structures reveal a protein fold consisting of two concentric β-barrels, tightly kept together by hydrophobic interactions. This fold suggests a basis for the prion-like ultrastability of aerolysin pore and its stoichiometry.
History
DepositionMay 17, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseJul 13, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5jzt
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8187.png

Downloads & links

-
Map

FileDownload / File: emd_8187.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationaerolysin WT pore in LMNG mmicelle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 150 pix.
= 252. Å		1.68 Å/pix.
x 150 pix.
= 252. Å		1.68 Å/pix.
x 150 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.26221958 - 0.4720648
Average (Standard dev.)0.0047801733 (±0.029325243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.2620.4720.005

-
Supplemental data

-
Sample components

-
Entire : aerolysin pore

EntireName: aerolysin pore
Components
  • Complex: aerolysin pore
    • Protein or peptide: Aerolysin

-
Supramolecule #1: aerolysin pore

SupramoleculeName: aerolysin pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Aerolysin oligomer in it's pore conformation in LMNG micelles.
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Molecular weightTheoretical: 350 KDa

-
Macromolecule #1: Aerolysin

MacromoleculeName: Aerolysin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Molecular weightTheoretical: 47.185152 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AEPVYPDQLR LFSLGQGVCG DKYRPVNREE AQSVKSNIVG MMGQWQISGL ANGWVIMGPG YNGEIKPGTA SNTWCYPTNP VTGEIPTLS ALDIPDGDEV DVQWRLVHDS ANFIKPTSYL AHYLGYAWVG GNHSQYVGED MDVTRDGDGW VIRGNNDGGC D GYRCGDKT ...String:
AEPVYPDQLR LFSLGQGVCG DKYRPVNREE AQSVKSNIVG MMGQWQISGL ANGWVIMGPG YNGEIKPGTA SNTWCYPTNP VTGEIPTLS ALDIPDGDEV DVQWRLVHDS ANFIKPTSYL AHYLGYAWVG GNHSQYVGED MDVTRDGDGW VIRGNNDGGC D GYRCGDKT AIKVSNFAYN LDPDSFKHGD VTQSDRQLVK TVVGWAVNDS DTPQSGYDVT LRYDTATNWS KTNTYGLSEK VT TKNKFKW PLVGETELSI EIAANQSWAS QNGGSTTTSL SQSVRPTVPA RSKIPVKIEL YKADISYPYE FKADVSYDLT LSG FLRWGG NAWYTHPDNR PNWNHTFVIG PYKDKASSIR YQWDKRYIPG EVKWWDWNWT IQQNGLSTMQ NNLARVLRPV RAGI TGDFS AESQFAGNIE IGAPVPLAA

UniProtKB: Aerolysin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: 30 seconds glow discharged grids, 4ul sample, 5 seconds blot.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 22.42 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 29079
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3c0n

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 27108
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3c0n


Chain - Chain ID: B / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-5jzt:
Cryo-EM structure of aerolysin pore in LMNG micelle

+
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