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- EMDB-9315: Cryo-EM structure of the HO BMC shell: subregion classified for B... -

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Basic information

Entry
Database: EMDB / ID: EMD-9315
TitleCryo-EM structure of the HO BMC shell: subregion classified for BMC-T: TS-TDTDTD
Map dataFour BMC-T positions classified: TS-TDTDTD
Sample
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Microcompartments protein
    • 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 microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / 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 ...Bacterial microcompartment shell protein PduT / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / 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 / Bacterial microcompartment protein trimer-2
Similarity search - Component
Biological speciesHaliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGreber BJ / Sutter M / Kerfeld CA
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 7, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseMar 13, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 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-6n0g
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9315.png

Downloads & links

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Map

FileDownload / File: emd_9315.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFour BMC-T positions classified: TS-TDTDTD
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-0.08656922 - 0.14542013
Average (Standard dev.)0.00013750707 (±0.0029908689)
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-0.0870.1450.000

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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
    • 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)
Strain: DSM 14365 / JCM 11303 / SMP-2
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 (strain DSM 14365 / JCM 11303 / SMP-2) (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 (strain DSM 14365 / JCM 11303 / SMP-2) (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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Macromolecule #3: Microcompartments protein

MacromoleculeName: Microcompartments protein / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 22.904137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN ...String:
MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN VTPYGAFGRL YLAGSEAEID AAAEAAEAAI RSVSGVAQES FRDR

UniProtKB: Bacterial microcompartment protein trimer-2

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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
GridSupport 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 / Details: unspecified
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 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4)
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 images used: 80783
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: 2 / Software - Name: RELION (ver. 1.4)
Details: Three sequential classifications for four BMC-T positions in total, using the symmetry expanded 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-6n0g:
Cryo-EM structure of the HO BMC shell: subregion classified for BMC-T: TS-TDTDTD

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