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- PDB-7yzy: pMMO structure from native membranes by cryoET and STA -

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Basic information

Entry
Database: PDB / ID: 7yzy
TitlepMMO structure from native membranes by cryoET and STA
Components
  • Methane monooxygenase subunit C2
  • Particulate methane monooxygenase alpha subunit
  • Particulate methane monooxygenase beta subunit
KeywordsMEMBRANE PROTEIN / pMMO / array / native membranes
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)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.8 Å
AuthorsZhu, Y. / Ni, T. / Zhang, P.
Funding support United Kingdom, 2items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Particulate methane monooxygenase beta subunit
C: Methane monooxygenase subunit C2
A: Particulate methane monooxygenase alpha subunit
F: Particulate methane monooxygenase beta subunit
G: Methane monooxygenase subunit C2
E: Particulate methane monooxygenase alpha subunit
J: Particulate methane monooxygenase beta subunit
K: Methane monooxygenase subunit C2
I: Particulate methane monooxygenase alpha subunit


Theoretical massNumber of molelcules
Total (without water)323,3679
Polymers323,3679
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Particulate methane monooxygenase beta subunit / Methane monooxygenase A subunit / Particulate methane monooxygenase 27 kDa subunit / Particulate ...Methane monooxygenase A subunit / Particulate methane monooxygenase 27 kDa subunit / Particulate methane monooxygenase hydroxylase 26 kDa subunit / Particulate methane monooxygenase hydroxylase beta subunit / pMMO-H beta subunit


Mass: 28445.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath
References: UniProt: Q607G3, methane monooxygenase (particulate)
#2: Protein Methane monooxygenase subunit C2 /


Mass: 33214.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / References: UniProt: O05111
#3: Protein Particulate methane monooxygenase alpha subunit / Methane monooxygenase B subunit / Particulate methane monooxygenase 45 kDa subunit / Particulate ...Methane monooxygenase B subunit / Particulate methane monooxygenase 45 kDa subunit / Particulate methane monooxygenase 47 kDa subunit / Particulate methane monooxygenase hydroxylase 45 kDa subunit / Particulate methane monooxygenase hydroxylase alpha subunit / pMMO-H alpha subunit


Mass: 46129.746 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath
References: UniProt: G1UBD1, methane monooxygenase (particulate)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: pMMO / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6000 nm / Nominal defocus min: 2500 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 129 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127417 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 187 / Num. of volumes extracted: 127417

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