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- PDB-9ksl: Cryo-EM structure of the family 2A encapsulin from Mycolicibacter... -

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Basic information

Entry
Database: PDB / ID: 9ksl
TitleCryo-EM structure of the family 2A encapsulin from Mycolicibacterium smegmatis
ComponentsMajor membrane protein I (MMP-I)
KeywordsVIRUS LIKE PARTICLE / Nanocompartment / Icosahedral shell / Cargo cysteine desulfurase loaded / Family 2A encapsulin
Function / homology: / Type 2A encapsulin shell protein SrpI-like / Type 2A encapsulin shell protein SrpI-like / Major membrane protein I (MMP-I)
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.81 Å
AuthorsMu, A. / Wang, P.P. / Wang, Q. / Rao, Z.H.
Funding support China, 7items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
Chinese Academy of SciencesXDB37020203 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
Ministry of Science and Technology (MoST, China)2020YFA0707500 China
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)31971118 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the family 2A encapsulin from Mycolicibacterium smegmatis
Authors: Mu, A. / Wang, P.P. / Wang, Q. / Rao, Z.H.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 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
A: Major membrane protein I (MMP-I)


Theoretical massNumber of molelcules
Total (without water)34,7541
Polymers34,7541
Non-polymers00
Water00
1
A: Major membrane protein I (MMP-I)
x 60


Theoretical massNumber of molelcules
Total (without water)2,085,23660
Polymers2,085,23660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Major membrane protein I (MMP-I)


Mass: 34753.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: MSMEI_4424 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FQA7
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: family 2A encapsulin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 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: 4.6 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6521
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPUimage acquisition
4cryoSPARC4.6.0CTF correction
7UCSF ChimeraX1.7model fitting
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
11cryoSPARC4.6.0classification
12cryoSPARC4.6.03D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 521821
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 1.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412784 / Algorithm: FOURIER SPACE / Num. of class averages: 7 / Symmetry type: POINT
Atomic model buildingB value: 61.9 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 1.81 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032385
ELECTRON MICROSCOPYf_angle_d0.5763269
ELECTRON MICROSCOPYf_dihedral_angle_d4.156328
ELECTRON MICROSCOPYf_chiral_restr0.048386
ELECTRON MICROSCOPYf_plane_restr0.004425

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