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Yorodumi- PDB-7s4l: CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s4l | ||||||
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Title | CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution | ||||||
Components | (Particulate methane monooxygenase, ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methylomicrobium alcaliphilum (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å | ||||||
Authors | Koo, C.W. / Rosenzweig, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2022 Title: Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Authors: Christopher W Koo / Frank J Tucci / Yuan He / Amy C Rosenzweig / Abstract: Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using ...Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s4l.cif.gz | 620.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s4l.ent.gz | 488.8 KB | Display | PDB format |
PDBx/mmJSON format | 7s4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s4l_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7s4l_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7s4l_validation.xml.gz | 94.1 KB | Display | |
Data in CIF | 7s4l_validation.cif.gz | 128 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/7s4l ftp://data.pdbj.org/pub/pdb/validation_reports/s4/7s4l | HTTPS FTP |
-Related structure data
Related structure data | 24830MC 7s4hC 7s4iC 7s4jC 7s4kC 7s4mC 7t4oC 7t4pC 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
-Particulate methane monooxygenase, ... , 3 types, 9 molecules ADEBFGCHI
#1: Protein | Mass: 45602.125 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria) Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z References: UniProt: G4SZ64, methane monooxygenase (soluble) #2: Protein | Mass: 28277.934 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria) Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z References: UniProt: G4SZ63, methane monooxygenase (soluble) #3: Protein | Mass: 28872.328 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria) Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z References: UniProt: G4SZ62, methane monooxygenase (soluble) |
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-Non-polymers , 5 types, 39 molecules
#4: Chemical | ChemComp-CU / #5: Chemical | ChemComp-HXG / #6: Chemical | ChemComp-D10 / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: pMMO complex in a POPC nanodisc / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Methylotuvimicrobium alcaliphilum 20Z (bacteria) |
Buffer solution | pH: 7.3 |
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 |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443800 / Symmetry type: POINT | ||||||||||||||||||||||||
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