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- EMDB-40717: particulate methane monooxygenase crosslinked with 4,4,4-trifluor... -
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Open data
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Basic information
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Title | particulate methane monooxygenase crosslinked with 4,4,4-trifluorobutanol bound | |||||||||||||||||||||
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![]() | Metalloenzyme / Inhibitor / Membrane Protein / Nanodiscs / Oxidoreductase | |||||||||||||||||||||
Function / homology | ![]() methane monooxygenase (particulate) / methane monooxygenase (soluble) / : / : / monooxygenase activity / membrane / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.18 Å | |||||||||||||||||||||
![]() | Tucci FJ / Rosenzweig AC | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Product analog binding identifies the copper active site of particulate methane monooxygenase. Authors: Frank J Tucci / Richard J Jodts / Brian M Hoffman / Amy C Rosenzweig / ![]() Abstract: Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of ...Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the Cu, Cu, and Cu sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the Cu site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating Cu and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps. | |||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
Images | ![]() | 185.6 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sr1MC ![]() 8oyiC ![]() 8sqwC ![]() 8sr4C ![]() 8sr5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.0582 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40717_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40717_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : particulate methane monooxygenase
+Supramolecule #1: particulate methane monooxygenase
+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: COPPER (II) ION
+Macromolecule #5: DECANE
+Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #7: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #8: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
+Macromolecule #9: 4,4,4-trifluorobutan-1-ol
+Macromolecule #10: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.55 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 890148 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |