[English] 日本語
Yorodumi
- EMDB-47525: Escherichia coli DyP peroxidase-loaded encapsulin shell -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47525
TitleEscherichia coli DyP peroxidase-loaded encapsulin shell
Map data
Sample
  • Complex: Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell
    • Protein or peptide: Bacteriocin
    • Protein or peptide: DyP peroxidase
KeywordsDye-decolorizing peroxidase / peroxidase / DyP / encapsulin / VIRUS LIKE PARTICLE
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Bacteriocin
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsAndreas MP / Ubilla NC / Giessen TW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: bioRxiv / Year: 2024
Title: Structural and biochemical characterization of a widespread enterobacterial peroxidase encapsulin.
Authors: Natalia C Ubilla-Rodriguez / Michael P Andreas / Tobias W Giessen /
Abstract: Encapsulins are self-assembling protein compartments found in prokaryotes and specifically encapsulate dedicated cargo enzymes. The most abundant encapsulin cargo class are Dye-decolorizing ...Encapsulins are self-assembling protein compartments found in prokaryotes and specifically encapsulate dedicated cargo enzymes. The most abundant encapsulin cargo class are Dye-decolorizing Peroxidases (DyPs). It has been previously suggested that DyP encapsulins are involved in oxidative stress resistance and bacterial pathogenicity due to DyPs' inherent ability to reduce and detoxify hydrogen peroxide while oxidizing a broad range of organic co-substrates. Here, we report the structural and biochemical analysis of a DyP encapsulin widely found across enterobacteria. Using bioinformatic approaches, we show that this DyP encapsulin is encoded by a conserved transposon-associated operon, enriched in enterobacterial pathogens. Through low pH and peroxide exposure experiments, we highlight the stability of this DyP encapsulin under harsh conditions and show that DyP catalytic activity is highest at low pH. We determine the structure of the DyP-loaded shell and free DyP via cryo-electron microscopy, revealing the structural basis for DyP cargo loading and peroxide preference. Our work lays the foundation to further explore the substrate range and physiological functions of enterobacterial DyP encapsulins.
History
DepositionOct 28, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47525.png

Downloads & links

-
Map

FileDownload / File: emd_47525.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.85 Å/pix.
x 384 pix.
= 325.901 Å		0.85 Å/pix.
x 384 pix.
= 325.901 Å		0.85 Å/pix.
x 384 pix.
= 325.901 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8487 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.010741 - 1.5417237
Average (Standard dev.)0.006865474 (±0.079311185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 325.9008 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_47525_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_47525_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell

EntireName: Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell
Components
  • Complex: Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell
    • Protein or peptide: Bacteriocin
    • Protein or peptide: DyP peroxidase

-
Supramolecule #1: Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell

SupramoleculeName: Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KTE40

-
Macromolecule #1: Bacteriocin

MacromoleculeName: Bacteriocin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KTE40
Molecular weightTheoretical: 28.846316 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNNLHRELAP VSDAAWEQIE EEATRTLKRF LAARRVVDVT DPQGAALSAV GTGHVAYLDG PCAGVSAVKR QVLPVVEFRV PFKLTRQAI DDVERGSQDS DWSPLKEAAR KIAAAEDQTI FDGYMAAGIA GIRPQSSNTP LTLPATASDY PTVVAQALDQ L RVAGVNGP ...String:
MNNLHRELAP VSDAAWEQIE EEATRTLKRF LAARRVVDVT DPQGAALSAV GTGHVAYLDG PCAGVSAVKR QVLPVVEFRV PFKLTRQAI DDVERGSQDS DWSPLKEAAR KIAAAEDQTI FDGYMAAGIA GIRPQSSNTP LTLPATASDY PTVVAQALDQ L RVAGVNGP YHLVLGEKAY TSITGGNEGG YPVFQHIRRL IDGEIVWAPA IEGGLLLTTR GGDFVMDIGQ DISIGYLNHT GT DVELYLQ ESFTFSALTS EATVTLLPPE E

UniProtKB: Bacteriocin

-
Macromolecule #2: DyP peroxidase

MacromoleculeName: DyP peroxidase / type: protein_or_peptide / ID: 2
Details: Residues 1-338 and 349-351 are not resolved. Residues 339-348 are the DyP-peroxidase targeting peptide.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KTE40
Molecular weightTheoretical: 38.531352 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGCPFSQSVS QPVDERLTRA AIFLVVTINP GKAAEVAVRA HCSILSSLIR GVGFRISDGG LSCVMGVSEG GWERLFGDTK PEYLHVFRE INGVHHAPST PGDLLYHIRA ARMDLCFELA SRILSDLGNS VSVVDSVQGF RYFDDRDLLG FVDGTENPVA Q AAVDATLI ...String:
MGCPFSQSVS QPVDERLTRA AIFLVVTINP GKAAEVAVRA HCSILSSLIR GVGFRISDGG LSCVMGVSEG GWERLFGDTK PEYLHVFRE INGVHHAPST PGDLLYHIRA ARMDLCFELA SRILSDLGNS VSVVDSVQGF RYFDDRDLLG FVDGTENPVA Q AAVDATLI GDEDMVFAGG SYVIVQKYLH DLDKWNAIPV EQQEKIIGRE KLSDIELRDA DKPSYAHNVL TSIEEDGEDV DI LRDNMPF GDPGKGEFGT YFIGYSRKPE RIERMLENMF IGNPPGNYDR ILDVSRAITG TLFFVPTTSF LDSIEPQSAP GQQ GDDVIN TLRSTAIKGD IMPGSLNIGS LKKEV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC7H17NO3TRIS(HYDROXYETHYL)AMINOMETHANE

Details: 150 mM NaCl, 20 mM Tris pH 7.5
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.
Details: Grids were glow discharged for 60 seconds at 5 mA under vacuum.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details: Grids were frozen with a blot force of 20, blot time of 4 seconds, 100% humidity, and chamber temperature of 22 degrees C..

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2065 / Average electron dose: 39.91 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 292965
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio model
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.1.2) / Software - details: homogeneous refinement
Details: Homogeneous refinement was used against an ab-initio map with I symmetry, per-particle defocus optimization enabled, per-group CTF parameter optimization enabled, and Ewald sphere correction ...Details: Homogeneous refinement was used against an ab-initio map with I symmetry, per-particle defocus optimization enabled, per-group CTF parameter optimization enabled, and Ewald sphere correction enabled using a positive curvature sign.
Number images used: 286236
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.1.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

nqk1

source_name: AlphaFold, initial_model_type: in silico model

an60

source_name: AlphaFold, initial_model_type: in silico model
DetailsThe AlphaFold model was placed using ChimeraX, followed by iterative manual refinement in Coot followed by Phenix real space refinements.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 85.5 / Target criteria: cross-correlation coefficient
Output model

PDB-9e5e:
Escherichia coli DyP peroxidase-loaded encapsulin shell

+
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