[English] 日本語
Yorodumi
- EMDB-50062: The structure of nonameric pore of RN1 variant of actinoporin Fav -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50062
TitleThe structure of nonameric pore of RN1 variant of actinoporin Fav
Map data
Sample
  • Complex: Nonameric RN1-Fav pore
    • Protein or peptide: Actinoporin
  • Ligand: Sphingomyelin C18
KeywordsActinoporin / Pore-forming toxin / Pore / nonamer / Transmembrane pore / TOXIN / Protein nanopore
Biological speciesOrbicella faveolata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsSolinc G / Srnko M / Anderluh G / Crnkovic A / Podobnik M
Funding support Slovenia, 3 items
OrganizationGrant numberCountry
Slovenian Research AgencyJ4-8225 Slovenia
Slovenian Research AgencyP1-0391 Slovenia
Other private
CitationJournal: To Be Published
Title: The structure of nonameric pore of RN1 variant of actinoporin Fav
Authors: Solinc G / Srnko M / Anderluh G / Crnkovic A / Podobnik M
History
DepositionApr 9, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50062.png

Downloads & links

-
Map

FileDownload / File: emd_50062.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 298. Å		0.75 Å/pix.
x 400 pix.
= 298. Å		0.75 Å/pix.
x 400 pix.
= 298. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.745 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-2.646829 - 3.311781
Average (Standard dev.)-0.00092128513 (±0.07020835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 298.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map B

Fileemd_50062_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_50062_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nonameric RN1-Fav pore

EntireName: Nonameric RN1-Fav pore
Components
  • Complex: Nonameric RN1-Fav pore
    • Protein or peptide: Actinoporin
  • Ligand: Sphingomyelin C18

-
Supramolecule #1: Nonameric RN1-Fav pore

SupramoleculeName: Nonameric RN1-Fav pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Nonameric Fav pore prepared on 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC):sphingomyelin (1:1 molar ratio) membranes
Source (natural)Organism: Orbicella faveolata (invertebrata)

-
Macromolecule #1: Actinoporin

MacromoleculeName: Actinoporin / type: protein_or_peptide / ID: 1
Details: This protein was expressed with an N-terminal deletion of 67 residues compared to the wild type. The deletion construct has three additional residues at the N-terminal (S) from the expression system.
Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Orbicella faveolata (invertebrata)
Molecular weightTheoretical: 21.307543 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SELDSENDAA DIAAGTIIAG AELTFGLLQN LLYFFANVNR KCAVGVDNES GFRWQEGSTY FFSGTADENL PYSVSDGYAV LYGPRKTNG PVATGVVGVL AYYIPSIGKT LAVMWSVPFD YNFYQNWWNA KLYSGNQRAD YDHYVDLYYN ANPFKANGWH E RSLGSGLK ...String:
SELDSENDAA DIAAGTIIAG AELTFGLLQN LLYFFANVNR KCAVGVDNES GFRWQEGSTY FFSGTADENL PYSVSDGYAV LYGPRKTNG PVATGVVGVL AYYIPSIGKT LAVMWSVPFD YNFYQNWWNA KLYSGNQRAD YDHYVDLYYN ANPFKANGWH E RSLGSGLK FCGSMSSSGQ ATLEIHVLKE SETCM

-
Macromolecule #2: Sphingomyelin C18

MacromoleculeName: Sphingomyelin C18 / type: ligand / ID: 2 / Number of copies: 45 / Formula: A1H8M
Molecular weightTheoretical: 732.089 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris
0.02 %Brij 35

Details: 150 mM NaCl, 50 mM Tris/HCl, 0.02 % Brij 35, pH 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 5147 / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 446027 / Details: Number of particles after template picking
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C9 (9 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 97704
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: Pore structure of the same protein from related entries
RefinementSpace: REAL
Output model

PDB-9eyq:
The structure of nonameric pore of RN1 variant of actinoporin Fav

+
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