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- PDB-6mzu: Cryo-EM structure of the HO BMC shell: BMC-TD focused structure, ... -

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Basic information

Entry
Database: PDB / ID: 6mzu
TitleCryo-EM structure of the HO BMC shell: BMC-TD focused structure, closed state
Components(Microcompartments proteinBacterial microcompartment) x 2
KeywordsSTRUCTURAL PROTEIN / microcompartment / shell / compartmentalization / BMC fold
Function / homologyMicrocompartment protein, bacteria / 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 (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 5, 2018 / Release: Mar 13, 2019

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Structure visualization

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Assembly

Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
D: Microcompartments protein
E: Microcompartments protein
F: 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)501,98742
Polyers501,98742
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Microcompartments protein / Bacterial microcompartment


Mass: 22904.137 Da / Num. of mol.: 6
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5816 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID6
#2: Protein/peptide ...
Microcompartments protein / Bacterial microcompartment


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacterial microcompartment shell from Haliangium ochraceum
Type: ORGANELLE OR CELLULAR COMPONENT / Source: RECOMBINANT
Molecular weightValue: 6.5 MDa / Experimental value: NO
Source (natural)Organism: Haliangium ochraceum (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: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins
Details: 5-7 sec incubation of the sample on the grid before blotting and plunging

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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: 5 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 25 e/Å2
Details: 928 images 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

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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIXmodel refinement
CTF correctionDetails: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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: 132076 / Algorithm: FOURIER SPACE
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.
Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Atomic model buildingPDB-ID: 5V74

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