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- EMDB-9311: Cryo-EM structure of the HO BMC shell: BMC-T1 in the assembled shell -

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Basic information

Entry
Database: EMDB / ID: EMD-9311
TitleCryo-EM structure of the HO BMC shell: BMC-T1 in the assembled shell
Map dataAsymmetric reconstruction, BMC-T1
Sample
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Microcompartments protein
    • Protein or peptide: Microcompartments protein
Keywordsmicrocompartment / shell / compartmentalization / BMC fold / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment shell protein PduT / 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 trimer-1 / Bacterial microcompartment protein homohexamer
Similarity search - Component
Biological speciesHaliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria) / Haliangium ochraceum DSM 14365 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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-FG02-91ER20021 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) releaseNov 21, 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: 0.03
  • 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-6n06
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9311.png

Downloads & links

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Map

FileDownload / File: emd_9311.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction, BMC-T1
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: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.10702681 - 0.18858975
Average (Standard dev.)0.00007825903 (±0.0028637243)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1070.1890.000

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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
Components
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Microcompartments protein
    • Protein or peptide: Microcompartments protein

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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 (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Molecular weightTheoretical: 6.5 MDa

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Macromolecule #1: Microcompartments protein

MacromoleculeName: Microcompartments protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum DSM 14365 (bacteria) / Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 21.923199 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDHAPERFDA TPPAGEPDRP ALGVLELTSI ARGITVADAA LKRAPSLLLM SRPVSSGKHL LMMRGQVAEV EESMIAAREI AGAGSGALL DELELPYAHE QLWRFLDAPV VADAWEEDTE SVIIVETATV CAAIDSADAA LKTAPVVLRD MRLAIGIAGK A FFTLTGEL ...String:
MDHAPERFDA TPPAGEPDRP ALGVLELTSI ARGITVADAA LKRAPSLLLM SRPVSSGKHL LMMRGQVAEV EESMIAAREI AGAGSGALL DELELPYAHE QLWRFLDAPV VADAWEEDTE SVIIVETATV CAAIDSADAA LKTAPVVLRD MRLAIGIAGK A FFTLTGEL ADVEAAAEVV RERCGARLLE LACIARPVDE LRGRLFF

UniProtKB: Bacterial microcompartment protein trimer-1

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Macromolecule #2: Microcompartments protein

MacromoleculeName: Microcompartments protein / type: protein_or_peptide / ID: 2 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum DSM 14365 (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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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:
ConcentrationNameFormula
20.0 mMTris-HCl
50.0 mMsodium chlorideNaCl
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 Gatan Solarus.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 5-7 second 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 were retained after inspection for image quality.
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 pixel box to match the pixel size and appropriate box size for the data.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4)
Details: The dataset was refined without masking and subsequently masked to reveal only the subregion of the BMC shell to which the focused classification had been applied.
Number images used: 177642
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 111067 / Software - Name: RELION (ver. 1.4)
Details: Focused 3D classification after symmetry expansion of the particle dataset

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Atomic model buiding 1

Initial model
PDB IDChain

5v74

source_name: PDB, initial_model_type: experimental model

5dih

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6n06:
Cryo-EM structure of the HO BMC shell: BMC-T1 in the assembled shell

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