+Open data
-Basic information
Entry | Database: PDB / ID: 6qn1 | ||||||
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Title | T=4 quasi-symmetric bacterial microcompartment particle | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / bacterial microcompartment / protein shell / GRM2 type microcompartment / EutN / ccmK / PduA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||
Authors | Kalnins, G. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Authors: Gints Kalnins / Eva-Emilija Cesle / Juris Jansons / Janis Liepins / Anatolij Filimonenko / Kaspars Tars / Abstract: Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, ...Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6qn1.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6qn1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6qn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qn1_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6qn1_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6qn1_validation.xml.gz | 434.2 KB | Display | |
Data in CIF | 6qn1_validation.cif.gz | 655.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/6qn1 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qn1 | HTTPS FTP |
-Related structure data
Related structure data | 4595MC 4596C 4597C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 9962.463 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ccmL, SAMEA4873648_04509 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A486QTH6 #2: Protein | Mass: 10309.946 Da / Num. of mol.: 180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J4R4X1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: T=4 quasi-symmetric bacterial microcompartment particle Type: COMPLEX Details: Bacterial microcompartment particle made by coexpression of shell proteins Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 2.45 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Klebsiella pneumoniae (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was purified with gel filtration | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 291 K / Details: blot for 4 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1400 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1316 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 62533 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45915 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 149.892 / Protocol: RIGID BODY FIT / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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