[English] 日本語
Yorodumi
- EMDB-50859: Single particle cryo-EM reconstruction of Bacillus Methanolicus e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50859
TitleSingle particle cryo-EM reconstruction of Bacillus Methanolicus encapsulin nano compartment
Map dataExperimental map
Sample
  • Complex: Encapsulin nano compartment
    • Protein or peptide: Bacteriocin
KeywordsEncapsulin / nanocompartment / HK97 / STRUCTURAL PROTEIN
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesBacillus methanolicus MGA3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsMarles-Wright J / McIver Z / Basle A / Ross J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2306768 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N005570/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)1801041 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of Bacillus methanolicus encapsulin nano compartment
Authors: Marles-Wright J / McIver Z / Basle A / Ross J
History
DepositionJul 2, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50859.png

Downloads & links

-
Map

FileDownload / File: emd_50859.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExperimental map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 768 pix.
= 769.024 Å		1 Å/pix.
x 768 pix.
= 769.024 Å		1 Å/pix.
x 768 pix.
= 769.024 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00133 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.04095137 - 0.19980167
Average (Standard dev.)-0.000011860029 (±0.010502967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 769.02405 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50859_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map

Fileemd_50859_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_50859_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_50859_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Encapsulin nano compartment

EntireName: Encapsulin nano compartment
Components
  • Complex: Encapsulin nano compartment
    • Protein or peptide: Bacteriocin

-
Supramolecule #1: Encapsulin nano compartment

SupramoleculeName: Encapsulin nano compartment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus methanolicus MGA3 (bacteria)
Molecular weightTheoretical: 7.7 MDa

-
Macromolecule #1: Bacteriocin

MacromoleculeName: Bacteriocin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus methanolicus MGA3 (bacteria)
Molecular weightTheoretical: 32.051186 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGKTQLFPDS PLTDQDFSQL DQTVIDTARR QLIGRRFIEL YGPLGRGIQS IFNDVFIENY EAKMDFQGSF DTDIETSKRV NYTIPLLYK DFVLYWRDLE QAKVLDIPID FSAAANAARD VAILEDQMIF YGSKEFDIPG LMNVKGRSTH LIGNWYESGN A FQDVVEAR ...String:
MGKTQLFPDS PLTDQDFSQL DQTVIDTARR QLIGRRFIEL YGPLGRGIQS IFNDVFIENY EAKMDFQGSF DTDIETSKRV NYTIPLLYK DFVLYWRDLE QAKVLDIPID FSAAANAARD VAILEDQMIF YGSKEFDIPG LMNVKGRSTH LIGNWYESGN A FQDVVEAR NKLLEMKHNG PFALVLSPEL YSLLHRVHKD TNVLEIEHVR ELVTDGVFQT PVLKGKTGVL VNTGRNNLDL AV SEDFDTA YLGEEGMNHP FRVYETVVLR IKRPSAICTL EDGGE

UniProtKB: Type 1 encapsulin shell protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
150.0 mMNaClsodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 15 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9558 / Average exposure time: 4.17 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.6 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 190000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

DetailsImages subjected to patch motion correction and patch CTF in CryoSPARC
Particle selectionNumber selected: 1058170
Details: Template based picking from initial 2D templates from 6000 particles
CTF correctionDetails: Patch CTF in CryoSparc / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model in CryoSPARC / Details: Ab inito with two classes
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Homogenous refinement with Ewald sphere correction / Number images used: 109840
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Homogeneous refinement in CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Details: Homogeneous refinement with Ewald sphere correction in CryoSPARC
Final 3D classificationNumber classes: 2 / Avg.num./class: 50000
FSC plot (resolution estimation)

+
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