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- EMDB-4595: T=4 quasi-symmetric bacterial microcompartment particle -

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Basic information

Entry
Database: EMDB / ID: EMD-4595
TitleT=4 quasi-symmetric bacterial microcompartment particle
Map data
Sample
  • Complex: T=4 quasi-symmetric bacterial microcompartment particle
    • Protein or peptide: Carbon dioxide concentrating mechanism protein CcmL
    • Protein or peptide: BMC domain-containing protein
Keywordsbacterial microcompartment / protein shell / GRM2 type microcompartment / EutN / ccmK / PduA / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain ...Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Bacterial microcompartment protein homohexamer / Carbon dioxide concentrating mechanism protein CcmL
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsKalnins G
CitationJournal: Nat Commun / Year: 2020
Title: Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles.
Authors: Gints Kalnins / Eva-Emilija Cesle / Juris Jansons / Janis Liepins / Anatolij Filimonenko / Kaspars Tars /
Abstract: Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, ...Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
History
DepositionFeb 8, 2019-
Header (metadata) releaseDec 25, 2019-
Map releaseDec 25, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0759
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0759
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qn1
  • Surface level: 0.0759
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qn1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4595.png

Downloads & links

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Map

FileDownload / File: emd_4595.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0759 / Movie #1: 0.0759
Minimum - Maximum-0.14660348 - 0.28130165
Average (Standard dev.)0.00032779842 (±0.017151771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1470.2810.000

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Supplemental data

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Half map: #1

Fileemd_4595_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4595_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 : T=4 quasi-symmetric bacterial microcompartment particle

EntireName: T=4 quasi-symmetric bacterial microcompartment particle
Components
  • Complex: T=4 quasi-symmetric bacterial microcompartment particle
    • Protein or peptide: Carbon dioxide concentrating mechanism protein CcmL
    • Protein or peptide: BMC domain-containing protein

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Supramolecule #1: T=4 quasi-symmetric bacterial microcompartment particle

SupramoleculeName: T=4 quasi-symmetric bacterial microcompartment particle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Bacterial microcompartment particle made by coexpression of shell proteins
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 2.45 MDa

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Macromolecule #1: Carbon dioxide concentrating mechanism protein CcmL

MacromoleculeName: Carbon dioxide concentrating mechanism protein CcmL / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 9.962463 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MILAKVTGHV VATQKCDELR GSNLLLITRL DDKQQPMKDQ TWVAVDNVGA GMHDIVLAEE YFALNKDRYK AMSVVAIVEK VFRDTEQE

UniProtKB: Carbon dioxide concentrating mechanism protein CcmL

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Macromolecule #2: BMC domain-containing protein

MacromoleculeName: BMC domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 10.309946 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKEALGLIET KGLVACIEAA DAMCKAANVE LIGYENVGSG LVTAMVKGDV GAVNAAVDSG VEAAKRIGKV VSSRVIARPH NDIEKIAGS TKHKSLRPHN A

UniProtKB: Bacterial microcompartment protein homohexamer

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaCl
20.0 mMTris-HCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.
DetailsSample was purified with 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: 1316 / Average exposure time: 1.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.4000000000000001 µm / 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: 62533
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: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 45915
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: 2 / Avg.num./class: 22957 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4n8x

chain_id: AA, source_name: PDB, initial_model_type: experimental model

4qiv

chain_id: AB, source_name: PDB, initial_model_type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 149.892
Output model

PDB-6qn1:
T=4 quasi-symmetric bacterial microcompartment particle

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