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- PDB-9sqr: Symmetry relaxed reconstruction of Rhodospirillum rubrum encapsul... -

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Basic information

Entry
Database: PDB / ID: 9sqr
TitleSymmetry relaxed reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin nanocompartment
Components
  • Encapsulated ferritin-like protein
  • Type 1 encapsulin shell 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 / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / Ferritin-like superfamily
Similarity search - Domain/homology
Type 1 encapsulin shell protein / Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 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
DepositionSep 23, 2025Deposition site: PDBE / Processing site: PDBE
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

Downloads & links

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Assembly

Deposited unit
A0: Type 1 encapsulin shell protein
A: Type 1 encapsulin shell protein
B: Type 1 encapsulin shell protein
C: Type 1 encapsulin shell protein
D: Type 1 encapsulin shell protein
E: Type 1 encapsulin shell protein
F: Type 1 encapsulin shell protein
G: Type 1 encapsulin shell protein
H: Type 1 encapsulin shell protein
I: Type 1 encapsulin shell protein
J: Type 1 encapsulin shell protein
K: Type 1 encapsulin shell protein
L: Type 1 encapsulin shell protein
M: Type 1 encapsulin shell protein
N: Type 1 encapsulin shell protein
O: Type 1 encapsulin shell protein
P: Type 1 encapsulin shell protein
Q: Type 1 encapsulin shell protein
R: Type 1 encapsulin shell protein
S: Type 1 encapsulin shell protein
T: Type 1 encapsulin shell protein
V: Type 1 encapsulin shell protein
W: Type 1 encapsulin shell protein
X: Type 1 encapsulin shell protein
Y: Type 1 encapsulin shell protein
Z: Type 1 encapsulin shell protein
AA: Type 1 encapsulin shell protein
BA: Type 1 encapsulin shell protein
CA: Type 1 encapsulin shell protein
DA: Type 1 encapsulin shell protein
EA: Type 1 encapsulin shell protein
FA: Type 1 encapsulin shell protein
GA: Type 1 encapsulin shell protein
HA: Type 1 encapsulin shell protein
IA: Type 1 encapsulin shell protein
JA: Type 1 encapsulin shell protein
KA: Type 1 encapsulin shell protein
LA: Type 1 encapsulin shell protein
MA: Type 1 encapsulin shell protein
NA: Type 1 encapsulin shell protein
OA: Type 1 encapsulin shell protein
PA: Type 1 encapsulin shell protein
QA: Type 1 encapsulin shell protein
RA: Type 1 encapsulin shell protein
SA: Type 1 encapsulin shell protein
TA: Type 1 encapsulin shell protein
UA: Type 1 encapsulin shell protein
VA: Type 1 encapsulin shell protein
WA: Type 1 encapsulin shell protein
XA: Type 1 encapsulin shell protein
YA: Type 1 encapsulin shell protein
ZA: Type 1 encapsulin shell protein
AB: Type 1 encapsulin shell protein
BB: Type 1 encapsulin shell protein
CB: Type 1 encapsulin shell protein
DB: Type 1 encapsulin shell protein
EB: Type 1 encapsulin shell protein
FB: Type 1 encapsulin shell protein
GB: Type 1 encapsulin shell protein
HB: Type 1 encapsulin shell protein
1: Encapsulated ferritin-like protein
2: Encapsulated ferritin-like protein
3: Encapsulated ferritin-like protein
4: Encapsulated ferritin-like protein
5: Encapsulated ferritin-like protein
6: Encapsulated ferritin-like protein
7: Encapsulated ferritin-like protein
8: Encapsulated ferritin-like protein
9: Encapsulated ferritin-like protein
10: Encapsulated ferritin-like protein
11: Encapsulated ferritin-like protein
12: Encapsulated ferritin-like protein
13: Encapsulated ferritin-like protein
14: Encapsulated ferritin-like protein
15: Encapsulated ferritin-like protein
16: Encapsulated ferritin-like protein
17: Encapsulated ferritin-like protein
18: Encapsulated ferritin-like protein
19: Encapsulated ferritin-like protein
20: Encapsulated ferritin-like protein


Theoretical massNumber of molelcules
Total (without water)2,090,19180
Polymers2,090,19180
Non-polymers00
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 ...
Type 1 encapsulin shell protein


Mass: 29765.936 Da / Num. of mol.: 60
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
#2: Protein
Encapsulated ferritin-like protein / EncFtn


Mass: 15211.720 Da / Num. of mol.: 20
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
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
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Rhodospirillum rubrum encapsulin complexCOMPLEXComplex of the encapsulin nanocompartment and 4 decamers of the encapsulated ferritin. Ordered targeting peptides from the latter are modelled.all0RECOMBINANT
2Rhodospirillum rubrum encapsulated ferritinCOMPLEX#11RECOMBINANT
3Rhodospirillum rubrum encapsulated ferritin localisation peptideCOMPLEXOrdered localisation peptide from the encapsulated ferritin#22RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112.4 MDaNO
210.15 MDaNO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rhodospirillum rubrum (bacteria)1085
42Rhodospirillum rubrum (bacteria)1085
53Rhodospirillum rubrum (bacteria)1085
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
42Escherichia coli BL21(DE3) (bacteria)469008
53Escherichia 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 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
5cryoSPARC4.7CTF correction
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: 346315
Details: Particles from icosahedral reconstruction of Encapsulin:Encapsulated Ferritin complex
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41954 / Algorithm: FOURIER SPACE
Details: Icosahedral reconstruction with symmetry relaxation by marginalization to reconstruct interior cargo density and encapculin shell.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 33.7 / 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
Displacement parametersBiso mean: 171.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027121756
ELECTRON MICROSCOPYf_angle_d0.6995165484
ELECTRON MICROSCOPYf_chiral_restr0.0319124
ELECTRON MICROSCOPYf_plane_restr0.00321684
ELECTRON MICROSCOPYf_dihedral_angle_d3.889617361

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