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- EMDB-9314: Cryo-EM structure of the HO BMC shell: subregion classified for B... -

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Basic information

Entry
Database: EMDB / ID: 9314
TitleCryo-EM structure of the HO BMC shell: subregion classified for BMC-T: TD-TSTSTS
Map dataFour BMC-T positions classified: TD-TSTSTS
SampleBacterial microcompartment shell from Haliangium ochraceum
  • (Microcompartments ...Bacterial microcompartment) x 3
Function / homologyMicrocompartment protein, bacteria / Polyhedral organelle shell protein PduT / Bacterial microcompartments protein, conserved site / CcmK-like superfamily / BMC domain / Bacterial microcompartiments proteins signature. / Microcompartments protein / Microcompartments protein / Microcompartments protein
Function and homology information
SourceHaliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsGreber BJ / Sutter M / Kerfeld CA
CitationJournal: Structure / Year: 2019
Title: The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly.
Authors: Basil J Greber / Markus Sutter / Cheryl A Kerfeld
Abstract: Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive ...Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive competitive advantages from their BMC-based catabolism, implicating BMCs as drug targets. BMC shells are of interest for bioengineering due to their diverse and selective permeability properties and because they self-assemble. A complete understanding of shell composition and organization is a prerequisite for biotechnological applications. Here, we report the cryoelectron microscopy structure of a BMC shell at 3.0-Å resolution, using an image-processing strategy that allowed us to determine the previously uncharacterized structural details of the interactions formed by the BMC-T and BMC-T shell subunits in the context of the assembled shell. We found unexpected structural plasticity among these interactions, resulting in distinct shell populations assembled from varying numbers of the BMC-T and BMC-T subunits. We discuss the implications of these findings on shell assembly and function.
Validation ReportPDB-ID: 6n0f

SummaryFull reportAbout validation report
DateDeposition: Nov 7, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n0f
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9314.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.03 Å/pix.
= 527.36 Å
512 pix
1.03 Å/pix.
= 527.36 Å
512 pix
1.03 Å/pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.07897486 - 0.12812415
Average (Standard dev.)0.0001128128 (0.0025366424)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 527.36 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z527.360527.360527.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0790.1280.000

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Supplemental data

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Sample components

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Entire Bacterial microcompartment shell from Haliangium ochraceum

EntireName: Bacterial microcompartment shell from Haliangium ochraceum
Number of components: 4

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Component #1: cellular-component, Bacterial microcompartment shell from Haliang...

Cellular-componentName: Bacterial microcompartment shell from Haliangium ochraceum
Recombinant expression: No
MassTheoretical: 6.5 MDa
SourceSpecies: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Microcompartments protein

ProteinName: Microcompartments proteinBacterial microcompartment / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 22.904137 kDa
SourceSpecies: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Microcompartments protein

ProteinName: Microcompartments proteinBacterial microcompartment / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 10.126718 kDa
SourceSpecies: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Microcompartments protein

ProteinName: Microcompartments proteinBacterial microcompartment / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 21.923199 kDa
SourceSpecies: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.4
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: 5-7 seconds incubation of the sample on the grid before blotting and plunging.

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 48543.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 928 / Sampling size: 5 microns
Details: 928 images retained after inspection for image quality.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 25580
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION
Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The selected particle subset was refined without masking and subsequently masked to reveal only the subregion of the BMC shell to which the focused classification had been applied.

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5V74, 5DIH
Output model

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