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- EMDB-59321: Single particle reconstruction of Rhodospirillum rubrum encapsula... -

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Basic information

Entry
Database: EMDB / ID: EMD-59321
TitleSingle particle reconstruction of Rhodospirillum rubrum encapsulated ferritin in encapsulin nano compartment
Map dataExperimental map
Sample
  • Complex: Encapsulated ferritin decamer
    • Protein or peptide: Encapsulated ferritin-like protein
  • Ligand: FE (III) ION
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 / Ferritin-like superfamily
Similarity search - Domain/homology
Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsMarles-Wright J / McIver Z / Ross J / McCorvie T / Basle A
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
DepositionAug 5, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59321.png

Downloads & links

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Map

FileDownload / File: emd_59321.map.gz / Format: CCP4 / Size: 216 MB / 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.)
1.13 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: 0.35
Minimum - Maximum-1.0012608 - 2.5654635
Average (Standard dev.)-0.00062614336 (±0.037876558)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_59321_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_59321_additional_1.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_59321_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_59321_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Encapsulated ferritin decamer

EntireName: Encapsulated ferritin decamer
Components
  • Complex: Encapsulated ferritin decamer
    • Protein or peptide: Encapsulated ferritin-like protein
  • Ligand: FE (III) ION

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Supramolecule #1: Encapsulated ferritin decamer

SupramoleculeName: Encapsulated ferritin decamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Encapsulated ferritin-like protein

MacromoleculeName: Encapsulated ferritin-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / 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

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

Details: 150 mM NaCl 50 mM Tris.HCl pH 8
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE
DetailsEncapsulated ferritin within encapsulin nano compartment

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / 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 / 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

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Image processing

Particle selectionNumber selected: 272846 / Details: Particles from sub-particle selection
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 272846
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Avg.num./class: 27000 / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
DetailsAb intio model produced in ModelAngelo Refined in Phenix.realspace refine
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-33bf:
Single particle reconstruction of Rhodospirillum rubrum encapsulated ferritin in encapsulin nano compartment

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