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

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Database: PDB / ID: 6n06
TitleCryo-EM structure of the HO BMC shell: BMC-T1 in the assembled shell
Components(Microcompartments proteinBacterial microcompartment) x 2
KeywordsSTRUCTURAL PROTEIN / microcompartment / shell / compartmentalization / BMC fold
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
Function and homology information
Specimen sourceHaliangium ochraceum DSM 14365 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsGreber, B.J. / Sutter, M. / Kerfeld, C.A.
Funding supportUnited States , 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases5 R01 AI114975-05United States
Department of Energy (United States)DE-FG02-91ER20021United 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2018 / Release: Mar 13, 2019

Structure visualization

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Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
GA: Microcompartments protein
GB: Microcompartments protein
GC: Microcompartments protein
GD: Microcompartments protein
GE: Microcompartments protein
GF: Microcompartments protein
HA: Microcompartments protein
HB: Microcompartments protein
HC: Microcompartments protein
HD: Microcompartments protein
HE: Microcompartments protein
HF: Microcompartments protein
IA: Microcompartments protein
IB: Microcompartments protein
IC: Microcompartments protein
ID: Microcompartments protein
IE: Microcompartments protein
IF: Microcompartments protein
JA: Microcompartments protein
JB: Microcompartments protein
JC: Microcompartments protein
JD: Microcompartments protein
JE: Microcompartments protein
JF: Microcompartments protein
KA: Microcompartments protein
KB: Microcompartments protein
KC: Microcompartments protein
KD: Microcompartments protein
KE: Microcompartments protein
KF: Microcompartments protein
LA: Microcompartments protein
LB: Microcompartments protein
LC: Microcompartments protein
LD: Microcompartments protein
LE: Microcompartments protein
LF: Microcompartments protein

Theoretical massNumber of molelcules
Total (without water)430,33139

  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)88930
ΔGint (kcal/M)-590
Surface area (Å2)132630


#1: Protein/peptide Microcompartments protein / Bacterial microcompartment / HO-5812

Mass: 21923.199 Da / Num. of mol.: 3
Source: (gene. exp.) Haliangium ochraceum DSM 14365 (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5812 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LHE3
#2: Protein/peptide ...
Microcompartments protein / Bacterial microcompartment / HO-5815

Mass: 10126.718 Da / Num. of mol.: 36
Source: (gene. exp.) Haliangium ochraceum DSM 14365 (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5815 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID5

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Bacterial microcompartment shell from Haliangium ochraceum
Molecular weightValue: 6.5 MDa / Experimental value: NO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTris-HCl1
250 mMsodium chlorideNaCl1
30.01 %NP-40 substitute1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Protochips C-flat 1.2/1.3 holey carbon grids were coated with a thin carbon film and plasma-cleaned using a Gatan Solarus.
Grid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins
Details: 5-7 second incubation of the sample on the grid before blotting and plunging

Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 48543 / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 25 e/Å2
Details: 928 images were retained after inspection for image quality.
Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 928
Image scansSampling size: 5 microns / Width: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30


SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
CTF correctionDetails: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION
Particle selectionDetails: 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
Number of particles selected: 31800
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 177642 / Algorithm: FOURIER SPACE
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 of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID

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