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- PDB-9rzm: Single particle reconstruction of Rhodospirillum rubrum encapsuli... -

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Basic information

Entry
Database: PDB / ID: 9rzm
TitleSingle particle reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin complex
ComponentsType 1 encapsulin shell protein
KeywordsSTRUCTURAL PROTEIN / Encapsulin / nanocompartment / encapsulated ferritin
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / iron ion transport / Type 1 encapsulin shell protein
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.41 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: To Be Published
Title: Single particle reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin complex
Authors: McIver, Z. / McCorvie, T.J. / Basle, A. / Marles-Wright, J.
History
DepositionJul 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 61


Theoretical massNumber of molelcules
Total (without water)1,815,72261
Polymers1,815,72261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1_555x,y,z1
point symmetry operation59
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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Rhodospirillum rubric encapsulin and encapsulated ferritinCOMPLEXall0RECOMBINANT
2Rhodospirillum rubrum encapsulinCOMPLEX1RECOMBINANT
3Rhodospirillum rubrum encapsulated ferritinCOMPLEX1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112.4 MDaNO
211.8 MDaNO
310.15 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rhodospirillum rubrum (bacteria)1085
32Rhodospirillum rubrum (bacteria)1085
43Rhodospirillum rubrum (bacteria)1085
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8 / Details: 150 mM NaCl, 50 mM Tris-HCl, pH 8.0
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: Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin
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: 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

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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 / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 7994

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2PHENIX1.21.2_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: 552744
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348411 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 104.6 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingDetails: model produced in ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 111.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00381913
ELECTRON MICROSCOPYf_angle_d0.72742597
ELECTRON MICROSCOPYf_chiral_restr0.0425304
ELECTRON MICROSCOPYf_plane_restr0.0045337
ELECTRON MICROSCOPYf_dihedral_angle_d4.7209270

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