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- EMDB-21810: Cryo-EM structure of engineered variant of the Encapsulin from Th... -

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Basic information

Entry
Database: EMDB / ID: EMD-21810
TitleCryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)
Map dataEncapsulin protein
Sample
  • Complex: Mutant Enapsulin protein
    • Protein or peptide: Encapsulin
  • Ligand: FLAVIN MONONUCLEOTIDE
KeywordsProteolysis / Cytolysis / Defense Response to Bacterium / Extracellular Region / HYDROLASE
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / iron ion transport / peptidase activity / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / :
Similarity search - Domain/homology
Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsWilliams E / Jenkins M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)US-NSF (CBET 1706891) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of engineered variant of the Encapsulin from Thermotoga maritima (TmE)
Authors: Williams E / Zhao H / Jenkins M / Juneja P / Lutz S
History
DepositionApr 17, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wkv
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wkv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21810.png

Downloads & links

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Map

FileDownload / File: emd_21810.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEncapsulin protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.06372584 - 0.106755
Average (Standard dev.)0.00032502474 (±0.004504463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0640.1070.000

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Supplemental data

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Sample components

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Entire : Mutant Enapsulin protein

EntireName: Mutant Enapsulin protein
Components
  • Complex: Mutant Enapsulin protein
    • Protein or peptide: Encapsulin
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Mutant Enapsulin protein

SupramoleculeName: Mutant Enapsulin protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: FMN bound to Encapsulin
Source (natural)Organism: Thermotoga maritima (bacteria)

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Macromolecule #1: Encapsulin

MacromoleculeName: Encapsulin / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 29.603766 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY ...String:
MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY TLVINTDRWI NFLGGEKRVE ECLRGGKIIT TPRIEDALVV SERGGDFKLI LGQDLSIGYE DREKDAVRLF IT ETFTFQV VNPEALILLK F

UniProtKB: Type 1 encapsulin shell protein

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Macromolecule #2: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 60 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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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

BufferpH: 7.5
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 69476
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 24401
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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