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- PDB-9i8e: Structure of Encapsulin from Dendrosporobacter quercicolus -

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Basic information

Entry
Database: PDB / ID: 9i8e
TitleStructure of Encapsulin from Dendrosporobacter quercicolus
ComponentsEncapsulin
KeywordsCYTOSOLIC PROTEIN / Encapsulin
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesDendrosporobacter quercicolus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBelyy, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mater Adv / Year: 2025
Title: Structure of Encapsulin from Arthrobacter sp.
Authors: Pecanac, O. / Belyy, A. / Martin, C. / Kleissen, R. / Fraaije, M. / Loncar, N.
History
DepositionFeb 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Encapsulin
D: Encapsulin
B: Encapsulin
A: Encapsulin


Theoretical massNumber of molelcules
Total (without water)120,1254
Polymers120,1254
Non-polymers00
Water00
1
C: Encapsulin
D: Encapsulin
B: Encapsulin
A: Encapsulin
x 60


Theoretical massNumber of molelcules
Total (without water)7,207,500240
Polymers7,207,500240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein
Encapsulin


Mass: 30031.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendrosporobacter quercicolus (bacteria)
Gene: SAMN04488502_10872 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G9WS71
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: Encapsulin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Dendrosporobacter quercicolus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4549 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002128820
ELECTRON MICROSCOPYf_angle_d0.604175140
ELECTRON MICROSCOPYf_dihedral_angle_d12.63246140
ELECTRON MICROSCOPYf_chiral_restr0.04520460
ELECTRON MICROSCOPYf_plane_restr0.00922800

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