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

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Basic information

Entry
Database: PDB / ID: 6n06
TitleCryo-EM structure of the HO BMC shell: BMC-T1 in the assembled shell
Components(Microcompartments protein) x 2
KeywordsSTRUCTURAL PROTEIN / microcompartment / shell / compartmentalization / BMC fold
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 DSM 14365 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGreber, B.J. / Sutter, M. / Kerfeld, C.A.
Funding support United States, 2items
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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

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
Polymers430,33139
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area88930 Å2
ΔGint-590 kcal/mol
Surface area132630 Å2

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Components

#1: Protein Microcompartments protein / HO-5812


Mass: 21923.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 ...
Microcompartments protein / HO-5815


Mass: 10126.718 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacterial microcompartment shell from Haliangium ochraceum
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
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 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 5-7 second incubation of the sample on the grid before blotting and plunging

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 48543 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / 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 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 928
Details: 928 images were retained after inspection for image quality.
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionDetails: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 31800
Details: 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. 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.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15V74

5v74

15V741PDBexperimental model
25DIH

5dih

15DIH2PDBexperimental model

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