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- EMDB-9309: Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction... -

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Basic information

Entry
Database: EMDB / ID: EMD-9309
TitleCryo-EM structure of the HO BMC shell: Icosahedral reconstruction (main population)
Map dataCryo-EM reconstruction of the HO BMC shell (icosahedral symmetry)
Sample
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
    • Protein or peptide: Microcompartments protein HO-5815
    • Protein or peptide: Microcompartments protein HO-5816
Keywordsmicrocompartment / shell / compartmentalization / BMC fold / STRUCTURAL PROTEIN / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / 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) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / 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 shell vertex protein / Bacterial microcompartment protein homohexamer / Bacterial microcompartment protein trimer-2
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria) / Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGreber BJ / Sutter M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 R01 AI114975-05 United States
Department of Energy (DOE, United States)DE-FG01-91ER20021 United States
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.
History
DepositionNov 6, 2018-
Header (metadata) releaseDec 5, 2018-
Map releaseMar 13, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mzx
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mzx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9309.png

Downloads & links

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Map

FileDownload / File: emd_9309.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the HO BMC shell (icosahedral symmetry)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.4511142 - 0.84809214
Average (Standard dev.)0.0040241475 (±0.042632665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.4510.8480.004

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Supplemental data

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Half map: Unfiltered half-map

Fileemd_9309_half_map_1.map
AnnotationUnfiltered half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map

Fileemd_9309_half_map_2.map
AnnotationUnfiltered half-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 : Bacterial microcompartment shell from Haliangium ochraceum

EntireName: Bacterial microcompartment shell from Haliangium ochraceum
Components
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
    • Protein or peptide: Microcompartments protein HO-5815
    • Protein or peptide: Microcompartments protein HO-5816

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Supramolecule #1: Bacterial microcompartment shell from Haliangium ochraceum

SupramoleculeName: Bacterial microcompartment shell from Haliangium ochraceum
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Haliangium ochraceum (bacteria)
Molecular weightTheoretical: 6.5 MDa

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Macromolecule #1: Ethanolamine utilization protein EutN/carboxysome structural prot...

MacromoleculeName: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 9.866319 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVLGKVVGTV VASRKEPRIE GLSLLLVRAC DPDGTPTGGA VVCADAVGAG VGEVVLYASG SSARQTEVTN NRPVDATIMA IVDLVEMGG DVRFRKD

UniProtKB: Bacterial microcompartment shell vertex protein

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Macromolecule #2: Microcompartments protein HO-5815

MacromoleculeName: Microcompartments protein HO-5815 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 10.126718 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADALGMIEV RGFVGMVEAA DAMVKAAKVE LIGYEKTGGG YVTAVVRGDV AAVKAATEAG QRAAERVGEV VAVHVIPRPH VNVDAALPL GRTPGMDKSA

UniProtKB: Bacterial microcompartment protein homohexamer

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Macromolecule #3: Microcompartments protein HO-5816

MacromoleculeName: Microcompartments protein HO-5816 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (bacteria) / Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 22.904137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN ...String:
MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN VTPYGAFGRL YLAGSEAEID AAAEAAEAAI RSVSGVAQES FRDR

UniProtKB: Bacterial microcompartment protein trimer-2

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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

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
20.0 mMTris-HCl
50.0 mMSodium chloride
0.01 %NP-40 substitute
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
Details: Protochips C-flat 1.2/1.3 holey carbon grids were coated with a thin carbon film and plasma cleaned using a Gatain Solarus.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 5-7 sec incubation of the sample on the grid before blotting and plunging.

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 928 / Average exposure time: 4.5 sec. / Average electron dose: 25.0 e/Å2
Details: 928 images retained after inspection for image quality. Frames were aligned and dose weighed using Motioncor2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 31800
Details: 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
Startup modelType of model: EMDB MAP
EMDB ID:

8747


Details: The reference was re-scaled and placed in a 512x512x512 voxel box to match the pixel size and appropriate box size for the data.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9)
Details: Frequency-limited refinement in FREALIGN, excluding spatial frequencies higher than 3.6 Angstroms to avoid over-fitting. Icosahedral symmetry was applied throughout the refinement procedure.
Number images used: 15779
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9)
Details: Final refinement in FREALIGN, using defocus refinement and Ewald sphere correction.
Final 3D classificationNumber classes: 4 / Avg.num./class: 7950 / Software - Name: RELION (ver. 1.4)
Details: Icosahedral symmetry was applied during the classification.

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Atomic model buiding 1

Initial modelPDB ID:

5v74


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6mzx:
Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction (main population)

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