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- EMDB-14399: pMMO structure from native membranes by cryoET and STA -

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Basic information

Entry
Database: EMDB / ID: EMD-14399
TitlepMMO structure from native membranes by cryoET and STA
Map datanative pMMO density map by cryoET and STA
Sample
  • Complex: pMMO
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Methane monooxygenase subunit C2
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
Function / homology
Function and homology information


methane monooxygenase (particulate) / monooxygenase activity / membrane / metal ion binding
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein
Similarity search - Domain/homology
Particulate methane monooxygenase alpha subunit / Methane monooxygenase subunit C2 / Particulate methane monooxygenase beta subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 4.8 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
DepositionFeb 21, 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_14399.png

Downloads & links

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Map

FileDownload / File: emd_14399.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnative pMMO density map by cryoET and STA
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.033427842 - 0.044732757
Average (Standard dev.)3.6458212e-15 (±0.002794002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 241.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : pMMO

EntireName: pMMO
Components
  • Complex: pMMO
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Methane monooxygenase subunit C2
    • Protein or peptide: Particulate methane monooxygenase alpha subunit

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Supramolecule #1: pMMO

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

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Macromolecule #1: Particulate methane monooxygenase beta subunit

MacromoleculeName: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria) / Strain: ATCC 33009 / NCIMB 11132 / Bath
Molecular weightTheoretical: 28.445098 KDa
SequenceString: MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH ...String:
MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH VPVEYNGMLM SIADIQGYNY VRTGTPEYIR MVEKGTLRTF GKDVAPVSAF FSAFMSILIY FMWHFIGRWF SN ERFLQST

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Macromolecule #2: Methane monooxygenase subunit C2

MacromoleculeName: Methane monooxygenase subunit C2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria) / Strain: ATCC 33009 / NCIMB 11132 / Bath
Molecular weightTheoretical: 33.21418 KDa
SequenceString: MHETKQGGEK RFTGAICRCS HRYNSMEVKM AATTIGGAAA AEAPLLDKKW LTFALAIYTV FYLWVRWYEG VYGWSAGLDS FAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRNL AALTPREELR RNFTHLVWLV AYAWAIYWGA SYFTEQDGTW H QTIVRDTD ...String:
MHETKQGGEK RFTGAICRCS HRYNSMEVKM AATTIGGAAA AEAPLLDKKW LTFALAIYTV FYLWVRWYEG VYGWSAGLDS FAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRNL AALTPREELR RNFTHLVWLV AYAWAIYWGA SYFTEQDGTW H QTIVRDTD FTPSHIIEFY LSYPIYIITG FAAFIYAKTR LPFFAKGISL PYLVLVVGPF MILPNVGLNE WGHTFWFMEE LF VAPLHYG FVIFGWLALA VMGTLTQTFY SFAQGGLGQS LCEAVDEGLI AK

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Macromolecule #3: Particulate methane monooxygenase alpha subunit

MacromoleculeName: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria) / Strain: ATCC 33009 / NCIMB 11132 / Bath
Molecular weightTheoretical: 46.129746 KDa
SequenceString: MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN ...String:
MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN PVTTLTGQTV DLENYNEGNT YFWHAFWFAI GVAWIGYWSR RPIFIPRLLM VDAGRADELV SATDRKVAMG FL AATILIV VMAMSSANSK YPITIPLQAG TMRGMKPLEL PAPTVSVKVE DATYRVPGRA MRMKLTITNH GNSPIRLGEF YTA SVRFLD SDVYKDTTGY PEDLLAEDGL SVSDNSPLAP GETRTVDVTA SDAAWEVYRL SDIIYDPDSR FAGLLFFFDA TGNR QVVQI DAPLIPSFM

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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: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 127417
ExtractionNumber tomograms: 187 / Number images used: 127417
Final angle assignmentType: MAXIMUM LIKELIHOOD

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