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- EMDB-14530: pMMO three trimer interaction map from native membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-14530
TitlepMMO three trimer interaction map from native membrane
Map datapMMO trimer-trimer map
Sample
  • Complex: pMMO
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsZhu Y / Ni T / Zhang P
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003339/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure and activity of particulate methane monooxygenase arrays in methanotrophs.
Authors: Yanan Zhu / Christopher W Koo / C Keith Cassidy / Matthew C Spink / Tao Ni / Laura C Zanetti-Domingues / Benji Bateman / Marisa L Martin-Fernandez / Juan Shen / Yuewen Sheng / Yun Song / ...Authors: Yanan Zhu / Christopher W Koo / C Keith Cassidy / Matthew C Spink / Tao Ni / Laura C Zanetti-Domingues / Benji Bateman / Marisa L Martin-Fernandez / Juan Shen / Yuewen Sheng / Yun Song / Zhengyi Yang / Amy C Rosenzweig / Peijun Zhang /
Abstract: Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase ...Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.
History
DepositionMar 14, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14530.png

Downloads & links

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Map

FileDownload / File: emd_14530.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationpMMO trimer-trimer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 100 pix.
= 268. Å		2.68 Å/pix.
x 100 pix.
= 268. Å		2.68 Å/pix.
x 100 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0131
Minimum - Maximum-0.04290736 - 0.045651875
Average (Standard dev.)6.1692256e-14 (±0.0033433964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1 map

Fileemd_14530_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map

Fileemd_14530_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pMMO

EntireName: pMMO
Components
  • Complex: pMMO

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Supramolecule #1: pMMO

SupramoleculeName: pMMO / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 62250
ExtractionNumber tomograms: 187 / Number images used: 127417
Final angle assignmentType: MAXIMUM LIKELIHOOD

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