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- EMDB-25683: CryoEM structure of Methylococcus capsulatus (Bath) pMMO treated ... -
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Open data
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Basic information
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Title | CryoEM structure of Methylococcus capsulatus (Bath) pMMO treated with potassium cyanide in a native lipid nanodisc at 3.65 Angstrom resolution | |||||||||
![]() | CryoEM structure of Methylococcus capsulatus (Bath) pMMO treated with potassium cyanide in a native lipid nanodisc at 3.65 angstrom resolution | |||||||||
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![]() | complex / 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: 3.65 Å | |||||||||
![]() | Koo CW / Rosenzweig AC | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 96.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.8 KB | Display | ![]() |
Images | ![]() | 126.9 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() | 90.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 642.1 KB | Display | ![]() |
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Full document | ![]() | 641.6 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t4oMC ![]() 7s4hC ![]() 7s4iC ![]() 7s4jC ![]() 7s4kC ![]() 7s4lC ![]() 7s4mC ![]() 7t4pC C: citing same article ( M: atomic model generated by this map |
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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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Annotation | CryoEM structure of Methylococcus capsulatus (Bath) pMMO treated with potassium cyanide in a native lipid nanodisc at 3.65 angstrom resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.511 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: CryoEM structure of Methylococcus capsulatus (Bath) pMMO treated...
File | emd_25683_additional_1.map | ||||||||||||
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Annotation | CryoEM structure of Methylococcus capsulatus (Bath) pMMO treated with potassium cyanide in a native lipid nanodisc at 3.65 angstrom resolution, unsharpened | ||||||||||||
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Density Histograms |
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Sample components
-Entire : pMMO complex in a native lipid nanodisc
Entire | Name: pMMO complex in a native lipid nanodisc |
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Components |
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-Supramolecule #1: pMMO complex in a native lipid nanodisc
Supramolecule | Name: pMMO complex in a native lipid nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Particulate methane monooxygenase alpha subunit
Macromolecule | Name: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 46.129746 KDa |
Sequence | String: MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN ...String: MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN PVTTLTGQTV DLENYNEGNT YFWHAFWFAI GVAWIGYWSR RPIFIPRLLM VDAGRADELV SATDRKVAMG FL AATILIV VMAMSSANSK YPITIPLQAG TMRGMKPLEL PAPTVSVKVE DATYRVPGRA MRMKLTITNH GNSPIRLGEF YTA SVRFLD SDVYKDTTGY PEDLLAEDGL SVSDNSPLAP GETRTVDVTA SDAAWEVYRL SDIIYDPDSR FAGLLFFFDA TGNR QVVQI DAPLIPSFM UniProtKB: Particulate methane monooxygenase alpha subunit |
-Macromolecule #2: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
Macromolecule | Name: Ammonia monooxygenase/methane monooxygenase, subunit C family protein type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.839309 KDa |
Sequence | String: MAATTIGGAA AAEAPLLDKK WLTFALAIYT VFYLWVRWYE GVYGWSAGLD SFAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRN LAALTPREEL RRNFTHLVWL VAYAWAIYWG ASYFTEQDGT WHQTIVRDTD FTPSHIIEFY LSYPIYIITG F AAFIYAKT ...String: MAATTIGGAA AAEAPLLDKK WLTFALAIYT VFYLWVRWYE GVYGWSAGLD SFAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRN LAALTPREEL RRNFTHLVWL VAYAWAIYWG ASYFTEQDGT WHQTIVRDTD FTPSHIIEFY LSYPIYIITG F AAFIYAKT RLPFFAKGIS LPYLVLVVGP FMILPNVGLN EWGHTFWFME ELFVAPLHYG FVIFGWLALA VMGTLTQTFY SF AQGGLGQ SLCEAVDEGL IAK UniProtKB: Ammonia monooxygenase/methane monooxygenase, subunit C family protein |
-Macromolecule #3: Particulate methane monooxygenase beta subunit
Macromolecule | Name: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.445098 KDa |
Sequence | String: MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH ...String: MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH VPVEYNGMLM SIADIQGYNY VRTGTPEYIR MVEKGTLRTF GKDVAPVSAF FSAFMSILIY FMWHFIGRWF SN ERFLQST UniProtKB: Particulate methane monooxygenase beta subunit |
-Macromolecule #4: COPPER (II) ION
Macromolecule | Name: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: CU |
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Molecular weight | Theoretical: 63.546 Da |
Chemical component information | ![]() ChemComp-CU: |
-Macromolecule #5: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 9 / Formula: P1O |
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Molecular weight | Theoretical: 566.728 Da |
Chemical component information | ![]() ChemComp-P1O: |
-Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE
Macromolecule | Name: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 6 / Number of copies: 3 / Formula: PLC |
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Molecular weight | Theoretical: 622.834 Da |
Chemical component information | ![]() ChemComp-PLC: |
-Macromolecule #7: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 7 / Number of copies: 9 / Formula: D10 |
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Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ![]() ChemComp-D10: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.3 |
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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: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |