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- EMDB-62552: Cryo-EM structure of the family 2A encapsulin from Mycolicibacter... -

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Basic information

Entry
Database: EMDB / ID: EMD-62552
TitleCryo-EM structure of the family 2A encapsulin from Mycolicibacterium smegmatis
Map data
Sample
  • Complex: family 2A encapsulin
    • Protein or peptide: Major membrane protein I (MMP-I)
KeywordsNanocompartment / Icosahedral shell / Cargo cysteine desulfurase loaded / Family 2A encapsulin / VIRUS LIKE PARTICLE
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 MC2 155 (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.81 Å
AuthorsMu A / Wang PP / Wang Q / Rao ZH
Funding support China, 7 items
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 PP / Wang Q / Rao ZH
History
DepositionNov 29, 2024-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62552.png

Downloads & links

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Map

FileDownload / File: emd_62552.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 500 pix.
= 376.4 Å		0.75 Å/pix.
x 500 pix.
= 376.4 Å		0.75 Å/pix.
x 500 pix.
= 376.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7528 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.530313 - 0.8856155
Average (Standard dev.)0.00042385893 (±0.038280476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 376.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62552_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62552_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62552_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : family 2A encapsulin

EntireName: family 2A encapsulin
Components
  • Complex: family 2A encapsulin
    • Protein or peptide: Major membrane protein I (MMP-I)

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Supramolecule #1: family 2A encapsulin

SupramoleculeName: family 2A encapsulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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

MacromoleculeName: Major membrane protein I (MMP-I) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Molecular weightTheoretical: 34.753934 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTSAQNESQA LGDLAARQLA NATKTVPQLS TITPRFLLHL LSWVPVEAGI YRVNRVVNPD RVAIHSEAGA GTEEPLPETY VDYETHPRE YTLRSISTLL DVHTRVSDLY SSPHDQVTQQ LRLTIETIKE RQEYELVNNP EYGLLAQATP EQTIQTLAGA P TPDDLDAL ...String:
MTSAQNESQA LGDLAARQLA NATKTVPQLS TITPRFLLHL LSWVPVEAGI YRVNRVVNPD RVAIHSEAGA GTEEPLPETY VDYETHPRE YTLRSISTLL DVHTRVSDLY SSPHDQVTQQ LRLTIETIKE RQEYELVNNP EYGLLAQATP EQTIQTLAGA P TPDDLDAL ITKVWKTPAF FLTHPLGVAA FGRECTYRGV PPPTVSMYGA QFITWRGIPI VPSDKVPVED GTTKFVLVRT GE ERQGVVG LFQPGLVGEQ APGLSVRFTG INRSAIASYL VTLYTSLAVL TDDALAVLDG VAVDQFHEYQ DYKDDDDK

UniProtKB: Major membrane protein I (MMP-I)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration13 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 6521 / Average exposure time: 4.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 521821
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 7 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 412784
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 60 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 61.9 / Target criteria: Cross-correlation coefficient
Output model

PDB-9ksl:
Cryo-EM structure of the family 2A encapsulin from Mycolicibacterium smegmatis

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