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- PDB-33bf: Single particle reconstruction of Rhodospirillum rubrum encapsula... -

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Basic information

Entry
Database: PDB / ID: 33bf
TitleSingle particle reconstruction of Rhodospirillum rubrum encapsulated ferritin in encapsulin nano compartment
ComponentsEncapsulated ferritin-like protein
KeywordsOXIDOREDUCTASE / Encapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsMarles-Wright, J. / McIver, Z. / Ross, J. / McCorvie, T. / Basle, A.
Funding support United Kingdom, 1items
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, 2026Deposition site: PDBE / Processing site: PDBE
SupersessionSep 2, 2026ID: 9S13
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Encapsulated ferritin-like protein
B: Encapsulated ferritin-like protein
C: Encapsulated ferritin-like protein
D: Encapsulated ferritin-like protein
E: Encapsulated ferritin-like protein
F: Encapsulated ferritin-like protein
G: Encapsulated ferritin-like protein
H: Encapsulated ferritin-like protein
I: Encapsulated ferritin-like protein
J: Encapsulated ferritin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,67620
Polymers152,11710
Non-polymers55810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Encapsulated ferritin-like protein / EncFtn


Mass: 15211.720 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: fer, Rru_A0973 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2RVS1, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Encapsulated ferritin decamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.12 MDaNO
210.15 MDaNO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 150 mM NaCl 50 mM Tris.HCl pH 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
250 mMTris1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Encapsulated ferritin within encapsulin nano compartment
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7994

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPUimage acquisition
4cryoSPARC4.7CTF correction
9cryoSPARC4.6initial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARC4.6classification
12cryoSPARC4.73D reconstruction
13PHENIX2.1_6048model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 272846 / Details: Particles from sub-particle selection
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272846 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: Ab intio model produced in ModelAngelo Refined in Phenix.realspace refine
Atomic model buildingSource name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 137.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00487850
ELECTRON MICROSCOPYf_angle_d0.765710680
ELECTRON MICROSCOPYf_chiral_restr0.03981200
ELECTRON MICROSCOPYf_plane_restr0.00381390
ELECTRON MICROSCOPYf_dihedral_angle_d3.62011020

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