+Open data
-Basic information
Entry | Database: PDB / ID: 7yzy | |||||||||
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Title | pMMO structure from native membranes by cryoET and STA | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / pMMO / array / native membranes | |||||||||
Function / homology | Function and homology information methane monooxygenase (particulate) / monooxygenase activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Methylococcus capsulatus str. Bath (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Zhu, Y. / Ni, T. / Zhang, P. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yzy.cif.gz | 945.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yzy.ent.gz | 787 KB | Display | PDB format |
PDBx/mmJSON format | 7yzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yzy_validation.pdf.gz | 988.5 KB | Display | wwPDB validaton report |
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Full document | 7yzy_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7yzy_validation.xml.gz | 91.8 KB | Display | |
Data in CIF | 7yzy_validation.cif.gz | 130.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/7yzy ftp://data.pdbj.org/pub/pdb/validation_reports/yz/7yzy | HTTPS FTP |
-Related structure data
Related structure data | 14399MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: pMMO / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Methylococcus capsulatus str. Bath (bacteria) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 2500 nm |
Image recording | Electron 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 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127417 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 187 / Num. of volumes extracted: 127417 |