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- EMDB-12253: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles -

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Basic information

Entry
Database: EMDB / ID: EMD-12253
TitleD3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
Map dataD3 fusion of pT=4 bacterial microcompartment particles
Sample
  • Complex: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
    • Protein or peptide: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein
    • Protein or peptide: cmcD/EutN BMC-P bacterial microcompartment protein
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsKalnins G / Cesle EE
Funding support Latvia, Czech Republic, 2 items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/4/20/705 Latvia
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: Protein Sci / Year: 2021
Title: Variety of size and form of GRM2 bacterial microcompartment particles.
Authors: Eva Emilija Cesle / Anatolij Filimonenko / Kaspars Tars / Gints Kalnins /
Abstract: Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi- ...Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi-permeable protein shell and an enzymatic core, they can enhance enzyme performance and protect the cell from harmful intermediates. With the ability to encapsulate non-native enzymes, BMCs show high potential for applied use. For this goal, a detailed look into shell form variability is significant to predict shell adaptability. Here we present four novel 3D cryo-EM maps of recombinant Klebsiella pneumoniae GRM2 BMC shell particles with the resolution in range of 9 to 22 Å and nine novel 2D classes corresponding to discrete BMC shell forms. These structures reveal icosahedral, elongated, oblate, multi-layered and polyhedral traits of BMCs, indicating considerable variation in size and form as well as adaptability during shell formation processes.
History
DepositionJan 25, 2021-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateApr 21, 2021-
Current statusApr 21, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12253.png

Downloads & links

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Map

FileDownload / File: emd_12253.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD3 fusion of pT=4 bacterial microcompartment particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.44 Å/pix.
x 300 pix.
= 732. Å		2.44 Å/pix.
x 300 pix.
= 732. Å		2.44 Å/pix.
x 300 pix.
= 732. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.047976166 - 0.07686969
Average (Standard dev.)2.7463266e-05 (±0.00679795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 732.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.442.442.44
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z732.000732.000732.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0480.0770.000

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Supplemental data

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Half map: #2

Fileemd_12253_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12253_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles

EntireName: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
Components
  • Complex: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
    • Protein or peptide: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein
    • Protein or peptide: cmcD/EutN BMC-P bacterial microcompartment protein

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Supramolecule #1: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles

SupramoleculeName: D3 fusion of pT=4 quasi-symmetric bacterial microcompartment particles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: bacterial microcompartment particle obtained by recombinant expression of pentameric EutN and hexameric cmcC subunits
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein

MacromoleculeName: cmcC/PduA/ccmK BMC-H bacterial microcompartment protein
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKEALGLIET KGLVACIEAA DAMCKAANVE LIGYENVGSG LVTAMVKGDV GAVNAAVDSG VEAAKRIGKV VSSRVIARPH NDIEKIAGST KHKSLRPHNA

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Macromolecule #2: cmcD/EutN BMC-P bacterial microcompartment protein

MacromoleculeName: cmcD/EutN BMC-P bacterial microcompartment protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MILAKVTGHV VATQKCDELR GSNLLLITRL DDKQQPMKDQ TWVAVDNVGA GMHDIVLAEE YFALNKDRYK AMSVVAIVEK VFRDTEQE

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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

Concentration2 mg/mL
BufferpH: 8 / Component:
ConcentrationFormula
300.0 mMNaCl
20.0 mMTris-HCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4s before plunging.
DetailsSample was purified with ultracentrifugation and gel filtration

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 3240 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 45252
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: INSILICO MODEL
In silico model: Made in Relion 3.0 using stochastic Gradient Descent (SGD) algorithm
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 913
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 1 / Avg.num./class: 913 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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