[English] 日本語
Yorodumi
- EMDB-5917: Encapsulin protein (EncA) from Myxococcus xanthus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5917
TitleEncapsulin protein (EncA) from Myxococcus xanthus
Map dataReconstruction of the encapsulin protein (EncA) from Myxococcus xanthus
Sample
  • Sample: Encapsulin protein (EncA) from Myxococcus xanthus
  • Protein or peptide: Encapsulin
Keywordsencapsulin / Myxococcus xanthus / HK-97 fold / protein-bound organelle / iron storage
Function / homologyType 1 encapsulin shell protein / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / peptidase activity / iron ion transport / intracellular iron ion homeostasis / defense response to bacterium / Type 1 encapsulin shell protein EncA
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsMcHugh CA / Fontana J / Lam AS / Cheng N / Aksyuk AA / Steven AC / Hoiczyk E
CitationJournal: EMBO J / Year: 2014
Title: A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress.
Authors: Colleen A McHugh / Juan Fontana / Daniel Nemecek / Naiqian Cheng / Anastasia A Aksyuk / J Bernard Heymann / Dennis C Winkler / Alan S Lam / Joseph S Wall / Alasdair C Steven / Egbert Hoiczyk /
Abstract: Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound ...Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
History
DepositionMar 10, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 30, 2014-
UpdateSep 10, 2014-
Current statusSep 10, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4pt2
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4pt2
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5917.png

Downloads & links

-
Map

FileDownload / File: emd_5917.map.gz / Format: CCP4 / Size: 335 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the encapsulin protein (EncA) from Myxococcus xanthus
Voxel sizeX=Y=Z: 1.102 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-5.19883728 - 22.0062809
Average (Standard dev.)0.0 (±0.936252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 493.69598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1021.1021.102
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z493.696493.696493.696
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-224-224-224
NC/NR/NS448448448
D min/max/mean-5.19922.006-0.000

-
Supplemental data

-
Sample components

-
Entire : Encapsulin protein (EncA) from Myxococcus xanthus

EntireName: Encapsulin protein (EncA) from Myxococcus xanthus
Components
  • Sample: Encapsulin protein (EncA) from Myxococcus xanthus
  • Protein or peptide: Encapsulin

-
Supramolecule #1000: Encapsulin protein (EncA) from Myxococcus xanthus

SupramoleculeName: Encapsulin protein (EncA) from Myxococcus xanthus / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1
Molecular weightTheoretical: 32 KDa

-
Macromolecule #1: Encapsulin

MacromoleculeName: Encapsulin / type: protein_or_peptide / ID: 1 / Name.synonym: EncA / Number of copies: 1 / Oligomeric state: Icosahedral / Recombinant expression: Yes
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622
Molecular weightTheoretical: 32 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET12a-3556
SequenceUniProtKB: Type 1 encapsulin shell protein EncA / GO: defense response to bacterium, peptidase activity / InterPro: Type 1 encapsulin shell protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2
GridDetails: 400 mesh carbon grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber temperature: 83 K / Instrument: LEICA KF80

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 57620 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.65 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER
DateDec 3, 2012
Image recordingDigitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 157 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each micrograph
Final two d classificationNumber classes: 1
Final angle assignmentDetails: bsoft
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: OTHER / Software - Name: bsoft
Details: Final map was calculated dividing particles into two independent data sets
Number images used: 14000
DetailsBsoft package was used.
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