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Yorodumi- PDB-7s4m: CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s4m | ||||||
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Title | CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at 2.42 Angstrom resolution | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Complex | ||||||
Function / homology | COPPER (II) ION / DECANE / DODECANE / 1,2-dihexanoyl-sn-glycero-3-phosphocholine Function and homology information | ||||||
Biological species | Methylocystis sp. ATCC 49242 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 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 | 7s4m.cif.gz | 488.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s4m.ent.gz | 406.7 KB | Display | PDB format |
PDBx/mmJSON format | 7s4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/7s4m ftp://data.pdbj.org/pub/pdb/validation_reports/s4/7s4m | HTTPS FTP |
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-Related structure data
Related structure data | 24831MC 7s4hC 7s4iC 7s4jC 7s4kC 7s4lC 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 ... , 2 types, 6 molecules AEIFBJ
#1: Protein | Mass: 42785.566 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) #2: Protein | Mass: 27796.467 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) |
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-Protein / Protein/peptide , 2 types, 6 molecules GCKDNH
#3: Protein | Mass: 27924.629 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) #4: Protein/peptide | Mass: 1635.006 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria) |
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-Non-polymers , 5 types, 63 molecules
#5: Chemical | ChemComp-CU / #6: Chemical | ChemComp-HXG / #7: Chemical | ChemComp-D10 / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 native lipid nanodisc / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: Methylocystis sp. ATCC 49242 (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 FIELDBright-field microscopy |
Image recording | Electron dose: 1.02 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490196 / Symmetry type: POINT |