[English] 日本語
Yorodumi
- EMDB-55116: Symmetry relaxed reconstruction of Rhodospirillum rubrum encapsul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55116
TitleSymmetry relaxed reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin nanocompartment
Map dataSymmetry relaxed map
Sample
  • Complex: Rhodospirillum rubrum encapsulin complex
    • Complex: Rhodospirillum rubrum encapsulated ferritin
      • Complex: Rhodospirillum rubrum encapsulated ferritin localisation peptide
        • Protein or peptide: Encapsulated ferritin-like protein
      • Protein or peptide: Type 1 encapsulin shell protein
KeywordsEncapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / metal ion binding
Similarity search - Function
Ferritin-like protein / : / EncFtn-like / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / Ferritin-like superfamily
Similarity search - Domain/homology
Type 1 encapsulin shell protein / Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsMcIver Z / McCorvie TJ / Basle A / Marles-Wright J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2306768 United Kingdom
CitationJournal: J Struct Biol / Year: 2026
Title: Single particle cryo-EM analysis of the Rhodospirillum rubrum encapsulin nanocompartment shows variable loading of encapsulated ferritin cargo proteins and differences in the fivefold pore.
Authors: Zak McIver / Didi He / Jennifer Ross / Marta Cozzaglio / Cecilia Piergentili / Aritha Dornau / Natasha Sumpner / Finn Brady / Kathleen Bialik / Thomas McCorvie / Claudia Sissi / Arnaud ...Authors: Zak McIver / Didi He / Jennifer Ross / Marta Cozzaglio / Cecilia Piergentili / Aritha Dornau / Natasha Sumpner / Finn Brady / Kathleen Bialik / Thomas McCorvie / Claudia Sissi / Arnaud Baslé / David J Clarke / Jon Marles-Wright /
Abstract: Encapsulins are self-assembling protein nanocompartments found in bacteria and archaea that encapsulate cargo enzymes to protect the cell from their toxic reaction products or intermediates. ...Encapsulins are self-assembling protein nanocompartments found in bacteria and archaea that encapsulate cargo enzymes to protect the cell from their toxic reaction products or intermediates. Developments in cryo-electron microscopy (cryo-EM) data processing strategies have enabled encapsulins and their cargo proteins to be investigated together in greater detail. In this study, we present the single particle cryo-EM structure of the Rhodospirillum rubrum encapsulin in both the presence and absence of its partner encapsulated ferritin (EncFtn). Single particle icosahedral reconstructions of empty and loaded encapsulins revealed a higher degree of conformational flexibility at the five-fold pore in the cargo loaded encapsulin. We applied a new non-point group averaging workflow to analyze the encapsulated ferritins within the encapsulin nanocompartment, to produce the first fully refined in situ atomic model of the EncFtn at 2.8 Å resolution. Masked 2D classification and particle subtraction demonstrate that cargo loading is heterogeneous in this recombinant complex, with the encapsulin able to house up to five of the decameric EncFtn complexes. Our data provides new insights into the dynamics and cargo arrangement in encapsulins and demonstrates an adaptable workflow for high resolution reconstruction of encapsulin cargoes.
History
DepositionSep 23, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55116.png

Downloads & links

-
Map

FileDownload / File: emd_55116.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetry relaxed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 384 pix.
= 432.576 Å		1.13 Å/pix.
x 384 pix.
= 432.576 Å		1.13 Å/pix.
x 384 pix.
= 432.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1265 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.17639184 - 0.42472765
Average (Standard dev.)0.00020513796 (±0.026099512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 432.576 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55116_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map

Fileemd_55116_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_55116_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_55116_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Rhodospirillum rubrum encapsulin complex

EntireName: Rhodospirillum rubrum encapsulin complex
Components
  • Complex: Rhodospirillum rubrum encapsulin complex
    • Complex: Rhodospirillum rubrum encapsulated ferritin
      • Complex: Rhodospirillum rubrum encapsulated ferritin localisation peptide
        • Protein or peptide: Encapsulated ferritin-like protein
      • Protein or peptide: Type 1 encapsulin shell protein

-
Supramolecule #1: Rhodospirillum rubrum encapsulin complex

SupramoleculeName: Rhodospirillum rubrum encapsulin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Complex of the encapsulin nanocompartment and 4 decamers of the encapsulated ferritin. Ordered targeting peptides from the latter are modelled.
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 150 KDa

-
Supramolecule #2: Rhodospirillum rubrum encapsulated ferritin

SupramoleculeName: Rhodospirillum rubrum encapsulated ferritin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rhodospirillum rubrum (bacteria)

-
Supramolecule #3: Rhodospirillum rubrum encapsulated ferritin localisation peptide

SupramoleculeName: Rhodospirillum rubrum encapsulated ferritin localisation peptide
type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2
Details: Ordered localisation peptide from the encapsulated ferritin
Source (natural)Organism: Rhodospirillum rubrum (bacteria)

-
Macromolecule #1: Type 1 encapsulin shell protein

MacromoleculeName: Type 1 encapsulin shell protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 29.765936 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNDLMRDLAP ISAKAWAEIE TEARGTLTVT LAARKVVDFK GPLGWDASSV SLGRTEALAE EPKAAGSAAV VTVRKRAVQP LIELCVPFT LKRAELEAIA RGASDADLDP VIEAARAIAI AEDRAVFHGF AAGGITGIGE ASAEHALDLP ADLADFPGVL V RALAVLRD ...String:
MNDLMRDLAP ISAKAWAEIE TEARGTLTVT LAARKVVDFK GPLGWDASSV SLGRTEALAE EPKAAGSAAV VTVRKRAVQP LIELCVPFT LKRAELEAIA RGASDADLDP VIEAARAIAI AEDRAVFHGF AAGGITGIGE ASAEHALDLP ADLADFPGVL V RALAVLRD RGVDGPYALV LGRTVYQQLM ETTTPGGYPV LQHVRRLFEG PLIWAPGVDG AMLISQRGGD FELTVGRDFS IG YHDHDAQ SVHLYLQESM TFRCLGPEAA VPLRGLSQAA TKA

UniProtKB: Type 1 encapsulin shell protein

-
Macromolecule #2: Encapsulated ferritin-like protein

MacromoleculeName: Encapsulated ferritin-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 15.21172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAQSSNSTHE PLEVLKEETV NRHRAIVSVM EELEAVDWYD QRVDASTDPE LTAILAHNRD EEKEHAAMTL EWLRRNDAKW AEHLRTYLF TEGPITAIEA ADTAGEGSGG DAAKGATAQG DGSLGIGSLK GEAALARPPR L

UniProtKB: Encapsulated ferritin-like protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
50.0 mMC4H11NO3Tris

Details: 150 mM NaCl, 50 mM Tris-HCl, pH 8.0
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 4 uL of sample was applied to the grids, which were then blotted 100% humidity blot force 5 wait time 10 s blot time 3 seconds.
DetailsComplex of Rhodospirillum rubrum encapsulin and encapsulated ferritin

-
Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 80.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 7994 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 346315
Details: Particles from icosahedral reconstruction of Encapsulin:Encapsulated Ferritin complex
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: C1 ab initio model from cryoSPARC with focus mask on Encapsulated ferritin cargo proteins
Details: 10 classes for ab initio with circular mask to remove encapsulin density.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7)
Details: Icosahedral reconstruction with symmetry relaxation by marginalization to reconstruct interior cargo density and encapculin shell.
Number images used: 41954
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationNumber classes: 10 / Avg.num./class: 23000 / Software - Name: cryoSPARC (ver. 4.7)
Details: 3D classes showing clear encapsulated ferritin complexes chosen for further analysis. A single class with four decamers of encapsulated ferritin chosen and taken forward for analysis.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: model produced in ModelAngelo
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 33.7 / Target criteria: Cross-correlation coefficient
Output model

PDB-9sqr:
Symmetry relaxed reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin nanocompartment

+
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