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

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Basic information

Entry
Database: PDB / ID: 9ry4
TitleSingle particle reconstruction of Rhodospirillum rubrum encapsulin
ComponentsType 1 encapsulin shell protein
KeywordsSTRUCTURAL PROTEIN / Encapsulin / nanocompartment / encapsulated ferritin
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsMcIver, Z. / McCorvie, T.J. / Basle, A. / Marles-Wright, J.
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
DepositionJul 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A0: Type 1 encapsulin shell protein


Theoretical massNumber of molelcules
Total (without water)29,7661
Polymers29,7661
Non-polymers00
Water00
1
A0: Type 1 encapsulin shell protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,785,95660
Polymers1,785,95660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A0: Type 1 encapsulin shell protein
x 5


  • icosahedral pentamer
  • 149 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)148,8305
Polymers148,8305
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A0: Type 1 encapsulin shell protein
x 6


  • icosahedral 23 hexamer
  • 179 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)178,5966
Polymers178,5966
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Type 1 encapsulin shell protein


Mass: 29765.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: enc, Rru_A0974 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2RVS0
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: Rhodospirillum rubrum encapsulin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: Sample in 50 mM Tris.HCl pH8, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
250 mMTrisC4H11NO31
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample purified by Size-exclusion on Sephacryl S400
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: blot force 5, wait time 10 s, and blot time 3 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPUimage acquisition
4cryoSPARC4.7CTF correction
7UCSF ChimeraX1.1model fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARC4.7initial Euler assignment
11cryoSPARC4.7final Euler assignment
12cryoSPARC4.7classification
13cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3438531 / Details: Blob picker
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639134 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 70 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross correlation / Details: Real space refinement in phenix
Atomic model buildingDetails: ModelAngelo model from sequence / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 68.96 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332018
ELECTRON MICROSCOPYf_angle_d0.46292744
ELECTRON MICROSCOPYf_chiral_restr0.04317
ELECTRON MICROSCOPYf_plane_restr0.0035360
ELECTRON MICROSCOPYf_dihedral_angle_d4.261286

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