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- EMDB-54372: Single particle reconstruction of Rhodospirillum rubrum encapsulin -

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Basic information

Entry
Database: EMDB / ID: EMD-54372
TitleSingle particle reconstruction of Rhodospirillum rubrum encapsulin
Map dataCryosparc map
Sample
  • Complex: Rhodospirillum rubrum encapsulin
    • Protein or peptide: Type 1 encapsulin shell protein
KeywordsEncapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 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
DepositionJul 14, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54372.png

Downloads & links

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Map

FileDownload / File: emd_54372.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.019355064 - 0.14040527
Average (Standard dev.)0.0010370236 (±0.007586906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54372_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_54372_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

Fileemd_54372_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_54372_half_map_2.map
AnnotationHalf map
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Histogram

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Sample components

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Entire : Rhodospirillum rubrum encapsulin

EntireName: Rhodospirillum rubrum encapsulin
Components
  • Complex: Rhodospirillum rubrum encapsulin
    • Protein or peptide: Type 1 encapsulin shell protein

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Supramolecule #1: Rhodospirillum rubrum encapsulin

SupramoleculeName: Rhodospirillum rubrum encapsulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: Type 1 encapsulin shell protein

MacromoleculeName: Type 1 encapsulin shell protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

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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 mMC4H11NO3Tris

Details: Sample in 50 mM Tris.HCl pH8, 150 mM NaCl
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 / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: blot force 5, wait time 10 s, and blot time 3 seconds.
DetailsSample purified by Size-exclusion on Sephacryl S400

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 42.0 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: 1.6 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3438531 / Details: Blob picker
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 / Details: C1 startup model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 639134
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: 9 / Avg.num./class: 71000 / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo model from sequence
DetailsReal space refinement in phenix
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 70 / Target criteria: Cross correlation
Output model

PDB-9ry4:
Single particle reconstruction of Rhodospirillum rubrum encapsulin

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