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Yorodumi- EMDB-24831: CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POP... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24831 | |||||||||
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Title | CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at 2.42 Angstrom resolution | |||||||||
Map data | CryoEM structure of Methylocystis species strain Rockwell pMMO in a POPC nanodisc at 2.42 angstrom resolution | |||||||||
Sample |
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Biological species | Methylocystis sp. ATCC 49242 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.42 Å | |||||||||
Authors | Koo CW / Rosenzweig AC | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24831.map.gz | 201 MB | EMDB map data format | |
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Header (meta data) | emd-24831-v30.xml emd-24831.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24831_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_24831.png | 116.4 KB | ||
Others | emd_24831_additional_1.map.gz | 23.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24831 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24831 | HTTPS FTP |
-Related structure data
Related structure data | 7s4mMC 7s4hC 7s4iC 7s4jC 7s4kC 7s4lC 7t4oC 7t4pC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24831.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CryoEM structure of Methylocystis species strain Rockwell pMMO in a POPC nanodisc at 2.42 angstrom resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.52 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: CryoEM structure of Methylocystis species strain Rockwell pMMO...
File | emd_24831_additional_1.map | ||||||||||||
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Annotation | CryoEM structure of Methylocystis species strain Rockwell pMMO in a POPC nanodisc at 2.42 angstrom resolution processed by deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : pMMO complex in a native lipid nanodisc
+Supramolecule #1: pMMO complex in a native lipid nanodisc
+Macromolecule #1: Particulate methane monooxygenase alpha subunit
+Macromolecule #2: Particulate methane monooxygenase beta subunit
+Macromolecule #3: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
+Macromolecule #4: Unidentified Helix
+Macromolecule #5: COPPER (II) ION
+Macromolecule #6: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
+Macromolecule #7: DECANE
+Macromolecule #8: DODECANE
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.02 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |