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- PDB-9fy6: Single particle cryo-EM reconstruction of Bacillus Methanolicus e... -

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Basic information

Entry
Database: PDB / ID: 9fy6
TitleSingle particle cryo-EM reconstruction of Bacillus Methanolicus encapsulin nano compartment
ComponentsBacteriocin
KeywordsSTRUCTURAL PROTEIN / Encapsulin / nanocompartment / HK97
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesBacillus methanolicus MGA3 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsMarles-Wright, J. / McIver, Z. / Basle, A. / Ross, J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2306768 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N005570/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)1801041 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of Bacillus methanolicus encapsulin nano compartment
Authors: Marles-Wright, J. / McIver, Z. / Basle, A. / Ross, J.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data 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
A: Bacteriocin
B: Bacteriocin
C: Bacteriocin
D: Bacteriocin


Theoretical massNumber of molelcules
Total (without water)128,2054
Polymers128,2054
Non-polymers00
Water00
1
A: Bacteriocin
B: Bacteriocin
C: Bacteriocin
D: Bacteriocin
x 60


  • defined by author&software
  • Evidence: electron microscopy, rota_matrix 1 0 0 rota_matrix 0 1 0 rota_matrix 0 0 1 tran_orth 0 0 0 rota_matrix 0.309 0.809 0.5 rota_matrix -0.809 0.5 -0.309 rota_matrix -0.5 -0.309 0.809 tran_orth - ...Evidence: electron microscopy, rota_matrix 1 0 0 rota_matrix 0 1 0 rota_matrix 0 0 1 tran_orth 0 0 0 rota_matrix 0.309 0.809 0.5 rota_matrix -0.809 0.5 -0.309 rota_matrix -0.5 -0.309 0.809 tran_orth -237.6284 622.1406 384.5119 rota_matrix -0.809 0.5 0.309 rota_matrix -0.5 -0.309 -0.809 rota_matrix -0.309 -0.809 0.5 tran_orth 384.5122 1006.6524 622.1407 rota_matrix -0.809 -0.5 -0.309 rota_matrix 0.5 -0.309 -0.809 rota_matrix 0.309 -0.809 0.5 tran_orth 1006.6526 622.14 384.5126 rota_matrix 0.309 -0.809 -0.5 rota_matrix 0.809 0.5 -0.309 rota_matrix 0.5 -0.309 0.809 tran_orth 769.0241 -0.0004 0.0004 rota_matrix -1 0 0 rota_matrix 0 -1 0 rota_matrix 0 0 1 tran_orth 769.024 769.024 0 rota_matrix -0.309 -0.809 0.5 rota_matrix 0.809 -0.5 -0.309 rota_matrix 0.5 0.309 0.809 tran_orth 622.1407 384.5124 -237.6283 rota_matrix 0.809 -0.5 0.309 rota_matrix 0.5 0.309 -0.809 rota_matrix 0.309 0.809 0.5 tran_orth 146.8843 384.5124 -237.6287 rota_matrix 0.809 0.5 -0.309 rota_matrix -0.5 0.309 -0.809 rota_matrix -0.309 0.809 0.5 tran_orth 0.0007 769.0241 -0.0006 rota_matrix -0.309 0.809 -0.5 rota_matrix -0.809 -0.5 -0.309 rota_matrix -0.5 0.309 0.809 tran_orth 384.5123 1006.6523 146.8832 rota_matrix -1 0 0 rota_matrix 0 1 0 rota_matrix 0 0 -1 tran_orth 769.023 -0.001 769.024 rota_matrix -0.309 0.809 -0.5 rota_matrix 0.809 0.5 0.309 rota_matrix 0.5 -0.309 -0.809 tran_orth 384.5106 -237.6283 622.1409 rota_matrix 0.809 0.5 -0.309 rota_matrix 0.5 -0.309 0.809 rota_matrix 0.309 -0.809 -0.5 tran_orth -0.0004 0.0009 769.0246 rota_matrix 0.809 -0.5 0.309 rota_matrix -0.5 -0.309 0.809 rota_matrix -0.309 -0.809 -0.5 tran_orth 146.8843 384.5122 1006.6527 rota_matrix -0.309 -0.809 0.5 rota_matrix -0.809 0.5 0.309 rota_matrix -0.5 -0.309 -0.809 tran_orth 622.1407 384.511 1006.6524 rota_matrix 1 0 0 rota_matrix 0 -1 0 rota_matrix 0 0 -1 tran_orth 0.001 769.0251 769.024 rota_matrix 0.309 -0.809 -0.5 rota_matrix -0.809 -0.5 0.309 rota_matrix -0.5 0.309 -0.809 tran_orth 769.0251 769.0234 769.0236 rota_matrix -0.809 -0.5 -0.309 rota_matrix -0.5 0.309 0.809 rota_matrix -0.309 0.809 -0.5 tran_orth 1006.652 146.8824 384.5115 rota_matrix -0.809 0.5 0.309 rota_matrix 0.5 0.309 0.809 rota_matrix 0.309 0.809 -0.5 tran_orth 384.5105 -237.6283 146.8833 rota_matrix 0.309 0.809 0.5 rota_matrix 0.809 -0.5 0.309 rota_matrix 0.5 0.309 -0.809 tran_orth -237.629 146.8851 384.5121 rota_matrix 0 1 0 rota_matrix 0 0 -1 rota_matrix -1 0 0 tran_orth 0 769.0246 769.0235 rota_matrix -0.5 0.309 -0.809 rota_matrix 0.309 -0.809 -0.5 rota_matrix -0.809 -0.5 0.309 tran_orth 769.0241 769.0241 769.0239 rota_matrix -0.309 -0.809 -0.5 rota_matrix 0.809 -0.5 0.309 rota_matrix -0.5 -0.309 0.809 tran_orth 1006.6524 146.8834 384.5119 rota_matrix 0.309 -0.809 0.5 rota_matrix 0.809 0.5 0.309 rota_matrix -0.5 0.309 0.809 tran_orth 384.5118 -237.6283 146.8832 rota_matrix 0.5 0.309 0.809 rota_matrix 0.309 0.809 -0.5 rota_matrix -0.809 0.5 0.309 tran_orth -237.6286 146.8842 384.5114 rota_matrix 0 -1 0 rota_matrix 0 0 1 rota_matrix -1 0 0 tran_orth 769.024 -0.0005 769.0235 rota_matrix -0.5 -0.309 0.809 rota_matrix 0.309 0.809 0.5 rota_matrix -0.809 0.5 -0.309 tran_orth 384.5111 -237.6287 622.1398 rota_matrix -0.309 0.809 0.5 rota_matrix 0.809 0.5 -0.309 rota_matrix -0.5 0.309 -0.809 tran_orth -0.0011 0.0007 769.0236 rota_matrix 0.309 0.809 -0.5 rota_matrix 0.809 -0.5 -0.309 rota_matrix -0.5 -0.309 -0.809 tran_orth 146.8833 384.513 1006.6524 rota_matrix 0.5 -0.309 -0.809 rota_matrix 0.309 -0.809 0.5 rota_matrix -0.809 -0.5 -0.309 tran_orth 622.1409 384.5123 1006.6523 rota_matrix 0 -1 0 rota_matrix 0 0 -1 rota_matrix 1 0 0 tran_orth 769.0251 769.0235 0.0005 rota_matrix 0.5 -0.309 -0.809 rota_matrix -0.309 0.809 -0.5 rota_matrix 0.809 0.5 0.309 tran_orth 622.1409 384.5111 -237.6283 rota_matrix 0.309 0.809 -0.5 rota_matrix -0.809 0.5 0.309 rota_matrix 0.5 0.309 0.809 tran_orth 146.8833 384.5117 -237.6283 rota_matrix -0.309 0.809 0.5 rota_matrix -0.809 -0.5 0.309 rota_matrix 0.5 -0.309 0.809 tran_orth -0.0001 769.0244 0.0004 rota_matrix -0.5 -0.309 0.809 rota_matrix -0.309 -0.809 -0.5 rota_matrix 0.809 -0.5 0.309 tran_orth 384.5128 1006.6527 146.8843 rota_matrix 0 1 0 rota_matrix 0 0 1 rota_matrix 1 0 0 tran_orth -0.001 0.0005 0.0005 rota_matrix 0.5 0.309 0.809 rota_matrix -0.309 -0.809 0.5 rota_matrix 0.809 -0.5 -0.309 tran_orth -237.628 622.1415 384.5127 rota_matrix 0.309 -0.809 0.5 rota_matrix -0.809 -0.5 -0.309 rota_matrix 0.5 -0.309 -0.809 tran_orth 384.5134 1006.6523 622.1409 rota_matrix -0.309 -0.809 -0.5 rota_matrix -0.809 0.5 -0.309 rota_matrix 0.5 0.309 -0.809 tran_orth 1006.653 622.139 384.5121 rota_matrix -0.5 0.309 -0.809 rota_matrix -0.309 0.809 0.5 rota_matrix 0.809 0.5 -0.309 tran_orth 769.0231 -0.0011 0.0002 rota_matrix 0 0 -1 rota_matrix 1 0 0 rota_matrix 0 -1 0 tran_orth 769.0235 0 769.0246 rota_matrix 0.809 -0.5 -0.309 rota_matrix 0.5 0.309 0.809 rota_matrix -0.309 -0.809 0.5 tran_orth 384.5119 -237.6283 622.1407 rota_matrix 0.5 -0.309 0.809 rota_matrix -0.309 0.809 0.5 rota_matrix -0.809 -0.5 0.309 tran_orth -0.0001 -0.0001 769.0239 rota_matrix -0.5 0.309 0.809 rota_matrix -0.309 0.809 -0.5 rota_matrix -0.809 -0.5 -0.309 tran_orth 146.8832 384.5118 1006.6523 rota_matrix -0.809 0.5 -0.309 rota_matrix 0.5 0.309 -0.809 rota_matrix -0.309 -0.809 -0.5 tran_orth 622.1398 384.5118 1006.6527 rota_matrix 0 0 1 rota_matrix -1 0 0 rota_matrix 0 -1 0 tran_orth 0.0005 769.024 769.0246 rota_matrix -0.809 -0.5 0.309 rota_matrix -0.5 0.309 -0.809 rota_matrix 0.309 -0.809 -0.5 tran_orth 769.0244 769.0231 769.0246 rota_matrix -0.5 -0.309 -0.809 rota_matrix 0.309 0.809 -0.5 rota_matrix 0.809 -0.5 -0.309 tran_orth 1006.6521 146.8825 384.5127 rota_matrix 0.5 0.309 -0.809 rota_matrix 0.309 0.809 0.5 rota_matrix 0.809 -0.5 0.309 tran_orth 384.5113 -237.6287 146.8843 rota_matrix 0.809 0.5 0.309 rota_matrix -0.5 0.309 0.809 rota_matrix 0.309 -0.809 0.5 tran_orth -237.6286 146.884 384.5126 rota_matrix 0 0 1 rota_matrix 1 0 0 rota_matrix 0 1 0 tran_orth -0.0005 0.001 -0.0005 rota_matrix 0.809 0.5 0.309 rota_matrix 0.5 -0.309 -0.809 rota_matrix -0.309 0.809 -0.5 tran_orth -237.628 622.1417 384.5115 rota_matrix 0.5 0.309 -0.809 rota_matrix -0.309 -0.809 -0.5 rota_matrix -0.809 0.5 -0.309 tran_orth 384.5129 1006.6527 622.1398 rota_matrix -0.5 -0.309 -0.809 rota_matrix -0.309 -0.809 0.5 rota_matrix -0.809 0.5 0.309 tran_orth 1006.6527 622.1399 384.5114 rota_matrix -0.809 -0.5 0.309 rota_matrix 0.5 -0.309 0.809 rota_matrix -0.309 0.809 0.5 tran_orth 769.0234 -0.0001 -0.0006 rota_matrix 0 0 -1 rota_matrix -1 0 0 rota_matrix 0 1 0 tran_orth 769.0246 769.023 -0.0005 rota_matrix -0.809 0.5 -0.309 rota_matrix -0.5 -0.309 0.809 rota_matrix 0.309 0.809 0.5 tran_orth 622.1398 384.5116 -237.6287 rota_matrix -0.5 0.309 0.809 rota_matrix 0.309 -0.809 0.5 rota_matrix 0.809 0.5 0.309 tran_orth 146.8832 384.5129 -237.6283 rota_matrix 0.5 -0.309 0.809 rota_matrix 0.309 -0.809 -0.5 rota_matrix 0.809 0.5 -0.309 tran_orth 0.0009 769.0251 0.0002 rota_matrix 0.809 -0.5 -0.309 rota_matrix -0.5 -0.309 -0.809 rota_matrix 0.309 0.809 -0.5 tran_orth 384.5135 1006.6524 146.8833
  • 7.69 MDa, 240 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)7,692,285240
Polymers7,692,285240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Bacteriocin


Mass: 32051.186 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methanolicus MGA3 (bacteria) / Gene: BMMGA3_02020 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3E3I1
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 nano compartment / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 7.7 MDa / Experimental value: NO
Source (natural)Organism: Bacillus methanolicus MGA3 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepesC8H18N2O4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 190000 X / Calibrated magnification: 190000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 600 nm / Calibrated defocus max: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.17 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9558

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
Image processingDetails: Images subjected to patch motion correction and patch CTF in CryoSPARC
CTF correctionDetails: Patch CTF in CryoSparc / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1058170
Details: Template based picking from initial 2D templates from 6000 particles
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109840 / Algorithm: FOURIER SPACE / Details: Homogenous refinement with Ewald sphere correction / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 117.89 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00248678
ELECTRON MICROSCOPYf_angle_d0.450611763
ELECTRON MICROSCOPYf_chiral_restr0.04161323
ELECTRON MICROSCOPYf_plane_restr0.00271536
ELECTRON MICROSCOPYf_dihedral_angle_d4.12981167

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