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- EMDB-24830: CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in... -
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Open data
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Basic information
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Title | CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution | |||||||||
![]() | CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z in a POPC nanodisc at 2.42 angstrom resolution | |||||||||
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![]() | Complex / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 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 | ![]() | 195.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.8 KB | Display | ![]() |
Images | ![]() | 122.1 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s4lMC ![]() 7s4hC ![]() 7s4iC ![]() 7s4jC ![]() 7s4kC ![]() 7s4mC ![]() 7t4oC ![]() 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 Methylotuvimicrobium alcaliphilum 20Z in a POPC nanodisc at 2.42 angstrom resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.525 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : pMMO complex in a POPC nanodisc
Entire | Name: pMMO complex in a POPC nanodisc |
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Components |
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-Supramolecule #1: pMMO complex in a POPC nanodisc
Supramolecule | Name: pMMO complex in a POPC nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Particulate methane monooxygenase, B subunit
Macromolecule | Name: Particulate methane monooxygenase, B subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble) |
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Source (natural) | Organism: ![]() Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z |
Molecular weight | Theoretical: 45.602125 KDa |
Sequence | String: MKIIKDKVAK LSFVALLVTV TAAMFYTPTA SAHGEKSQAA FMRMRTIHWF DLNWSKDQVS VNETMSISGK FHVFAGWPET VDKPEVAFL NIGIPGPVFI RAGSWIGGQL VPRSVSLELG ETYEFKVLLK ARRPGDWHVH TMMNVQGGGP IIGPGKWVTI T GSMGDFKN ...String: MKIIKDKVAK LSFVALLVTV TAAMFYTPTA SAHGEKSQAA FMRMRTIHWF DLNWSKDQVS VNETMSISGK FHVFAGWPET VDKPEVAFL NIGIPGPVFI RAGSWIGGQL VPRSVSLELG ETYEFKVLLK ARRPGDWHVH TMMNVQGGGP IIGPGKWVTI T GSMGDFKN PITTLTGETI DLETYALDGV YGWHLFWYLL GVAWMVYWCR KPVFIPRRIA VDAGKADSLI TPTDKKVGMA FA AGTLAIV AVSMGQANEK YPVTTPLQAG LMRGIKSLEL PQPTVSVKVV DASYRVPGRA MQMTLEITNN GDSAVRLAEF NTA SVRFLD ADVYEDDTNY PDDLLAEEGL SVSDNSPLAP GETRTVDVTA SDAAWEVYRL ADLIYDPDSR FAGLLFFIDE DGNR QMTMV DAPLIPTFI UniProtKB: Particulate methane monooxygenase, B subunit |
-Macromolecule #2: Particulate methane monooxygenase, A subunit
Macromolecule | Name: Particulate methane monooxygenase, A subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble) |
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Source (natural) | Organism: ![]() Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z |
Molecular weight | Theoretical: 28.277934 KDa |
Sequence | String: MSASQSAVRS RAEAVKVSRT FDYMILFTVF FVVLGGYHIH YMLTGGDWDF WTDWKDRRLW VTVAPIVSIT FPAAVQAVLW WRYRIAWGA TLCVLGLLLG EWINRYFNFW GWTYFPVNFV FPSNLMPGAI VLDVILMLSN SMTLTAVVGG LAWGLLFYPG N WPIIAPLH ...String: MSASQSAVRS RAEAVKVSRT FDYMILFTVF FVVLGGYHIH YMLTGGDWDF WTDWKDRRLW VTVAPIVSIT FPAAVQAVLW WRYRIAWGA TLCVLGLLLG EWINRYFNFW GWTYFPVNFV FPSNLMPGAI VLDVILMLSN SMTLTAVVGG LAWGLLFYPG N WPIIAPLH VPVEYNGMMM TLADLQGYHY VRTGTPEYIR MVEKGTLRTF GKDVAPVSAF FSGFVSILIY FLWHFFGSWF GS EKFVQAA UniProtKB: Particulate methane monooxygenase, A subunit |
-Macromolecule #3: Particulate methane monooxygenase, C subunit
Macromolecule | Name: Particulate methane monooxygenase, C subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble) |
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Source (natural) | Organism: ![]() Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z |
Molecular weight | Theoretical: 28.872328 KDa |
Sequence | String: MAATTESVKA DAAEAPLLNK KNIIAGASLY LVFYAWVRWY EGVYGWSAGL DSFAPEFETY WMNFLYIEMV LEVLVASVLW GYIWKSRDR KVMSITPREE LRRHFTHWTW LMMYGIAIYF GASYFTEQDG TWHQTIVRDT DFTPSHIIEF YLSYPIYIIT G GASFLYAK ...String: MAATTESVKA DAAEAPLLNK KNIIAGASLY LVFYAWVRWY EGVYGWSAGL DSFAPEFETY WMNFLYIEMV LEVLVASVLW GYIWKSRDR KVMSITPREE LRRHFTHWTW LMMYGIAIYF GASYFTEQDG TWHQTIVRDT DFTPSHIIEF YLSYPIYIIT G GASFLYAK TRLPTYQQGL SLQYLVVVVG PFMILPNVGL NEWGHTFWFM EELFVAPLHY GFVFFGWSAL GVLGVINIEL GA LSKLLKK DLA UniProtKB: Particulate methane monooxygenase, C subunit |
-Macromolecule #4: COPPER (II) ION
Macromolecule | Name: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 9 / Formula: CU |
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Molecular weight | Theoretical: 63.546 Da |
Chemical component information | ![]() ChemComp-CU: |
-Macromolecule #5: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1,2-dihexanoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 15 / Formula: HXG |
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Molecular weight | Theoretical: 454.515 Da |
Chemical component information | ![]() ChemComp-HXG: |
-Macromolecule #6: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 6 / Number of copies: 9 / Formula: D10 |
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Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ![]() ChemComp-D10: |
-Macromolecule #7: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate
Macromolecule | Name: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate type: ligand / ID: 7 / Number of copies: 3 / Formula: 6ER |
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Molecular weight | Theoretical: 454.515 Da |
Chemical component information | ![]() ChemComp-6ER: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 3 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-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: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |