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Yorodumi- EMDB-31327: CryoEM structure of particulate methane monooxygenase associated ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31327 | |||||||||
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Title | CryoEM structure of particulate methane monooxygenase associated with Cu(I) (form 1) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information methane monooxygenase (particulate) / methane monooxygenase (soluble) / : / : / monooxygenase activity / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Methylococcus capsulatus str. Bath (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Chang WH / Lin HH / Huang SH / Chung SC | |||||||||
Citation | Journal: J Am Chem Soc / Year: 2021 Title: Copper Centers in the Cryo-EM Structure of Particulate Methane Monooxygenase Reveal the Catalytic Machinery of Methane Oxidation. Authors: W-H Chang / H-H Lin / I-K Tsai / S-H Huang / S-C Chung / I-P Tu / S S-F Yu / S I Chan / Abstract: The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room ...The particulate methane monooxygenase (pMMO) is the first enzyme in the C1 metabolic pathway in methanotrophic bacteria. As this enzyme converts methane into methanol efficiently near room temperature, it has become the paradigm for developing an understanding of this difficult C1 chemistry. pMMO is a membrane-bound protein with three subunits (PmoB, PmoA, and PmoC) and 12-14 coppers distributed among different sites. X-ray crystal structures that have revealed only three mononuclear coppers at three sites have neither disclosed the location of the active site nor the catalytic mechanism of the enzyme. Here we report a cyro-EM structure of -pMMO from (Bath) at 2.5 Å, and develop quantitative electrostatic-potential profiling to scrutinize the nonprotein densities for signatures of the copper cofactors. Our results confirm a mononuclear Cu at the site, resolve two Cus at the site, and uncover additional Cu clusters at the PmoA/PmoC interface within the membrane ( site) and in the water-exposed -terminal subdomain of the PmoB ( clusters). These findings complete the minimal set of copper factors required for catalytic turnover of pMMO, offering a glimpse of the catalytic machinery for methane oxidation according to the chemical principles underlying the mechanism proposed earlier. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31327.map.gz | 306.6 MB | EMDB map data format | |
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Header (meta data) | emd-31327-v30.xml emd-31327.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31327_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_31327.png | 135.6 KB | ||
Others | emd_31327_half_map_1.map.gz emd_31327_half_map_2.map.gz | 301.9 MB 301.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31327 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31327 | HTTPS FTP |
-Validation report
Summary document | emd_31327_validation.pdf.gz | 479.2 KB | Display | EMDB validaton report |
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Full document | emd_31327_full_validation.pdf.gz | 478.7 KB | Display | |
Data in XML | emd_31327_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_31327_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31327 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31327 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31327.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_31327_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31327_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : particulate methane monooxygenase (pMMO)
Entire | Name: particulate methane monooxygenase (pMMO) |
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Components |
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-Supramolecule #1: particulate methane monooxygenase (pMMO)
Supramolecule | Name: particulate methane monooxygenase (pMMO) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Methylococcus capsulatus str. Bath (bacteria) / Location in cell: membrane |
Molecular weight | Theoretical: 312 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Sugar embedding | Material: vitrified ice |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 278 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-60 / Number real images: 23484 / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |