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- EMDB-75807: Particulate methane monooxygenase in membrane arrays -

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Basic information

Entry
Database: EMDB / ID: EMD-75807
TitleParticulate methane monooxygenase in membrane arrays
Map data
Sample
  • Organelle or cellular component: particulate methane monooxygenase in native membrane arrays
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Particulate methane monooxygenase gamma subunit
  • Ligand: COPPER (II) ION
  • Ligand: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
  • Ligand: water
Keywordsparticulate methane monooxygenase / OXIDOREDUCTASE
Function / homology
Function and homology information


methane monooxygenase (particulate) / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / monooxygenase activity / membrane / metal ion binding
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein
Similarity search - Domain/homology
Particulate methane monooxygenase alpha subunit / Ammonia monooxygenase/methane monooxygenase, subunit C family protein / Particulate methane monooxygenase beta subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsTucci FJ / Miller CG / Rosenzweig AC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J Biol Chem / Year: 2026
Title: Membrane properties modulate methane oxidation by particulate methane monooxygenase.
Authors: Callie G Miller / Frank J Tucci / Genevieve R Nemeth / Sergey Stolyar / Mary E Lidstrom / Amy C Rosenzweig /
Abstract: The copper-dependent membrane monooxygenases particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) oxidize methane to methanol and ammonia to hydroxylamine, respectively. These ...The copper-dependent membrane monooxygenases particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) oxidize methane to methanol and ammonia to hydroxylamine, respectively. These enzymes, which are important targets for biotechnology, reside in intracytoplasmic membranes (ICMs) where they form densely packed hexagonal arrays. While cryoEM structures of pMMO and AMO in ICMs have revealed closely-associated lipids, little is known about how specific lipids and membrane morphologies influence activity. Here we show through cryoelectron tomography (cryoET) that three species of methane- and ammonia-oxidizing bacteria exhibit different types of ICM ultrastructure. Reconstitution of Methylococcus capsulatus (Bath) pMMO into liposomes replicated the array structure, allowing a systematic dissection of how liposome diameter and composition affect activity. Proteoliposome activity is inversely correlated with liposome size, suggesting that pMMO activity may be higher in membranes with increased surface curvature. Further, a comparison of lipids isolated from methanotrophs (native lipids), phosphatidylcholine (PC), and phosphoethanolamine (PE) showed that PE confers increased activity, with maximal activity observed for unsaturated PEs. Methane solubility measurements indicate that these enhancements are specific to pMMO. Cardiolipin further increases activity, consistent with its enrichment in M. capsulatus (Bath) cells. To assess pMMO-pMMO interactions in the ICMs, a 6 Å resolution cryoelectron microscopy (cryoEM) structure of three neighboring pMMO trimers was determined, revealing their arrangement in the array as well as specific residues and lipids mediating interaction interfaces. Taken together, these findings provide insight into the impact of the membrane environment on pMMO function and establish a platform for examining pMMOs and AMOs in tunable lipid environments.
History
DepositionMar 3, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75807.png

Downloads & links

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Map

FileDownload / File: emd_75807.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.14 Å/pix.
x 160 pix.
= 342.144 Å		2.14 Å/pix.
x 160 pix.
= 342.144 Å		2.14 Å/pix.
x 160 pix.
= 342.144 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1384 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.251
Minimum - Maximum-0.58506703 - 1.0873086
Average (Standard dev.)0.024192415 (±0.06698817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 342.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75807_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_75807_half_map_2.map
Projections & Slices
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Sample components

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Entire : particulate methane monooxygenase in native membrane arrays

EntireName: particulate methane monooxygenase in native membrane arrays
Components
  • Organelle or cellular component: particulate methane monooxygenase in native membrane arrays
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Particulate methane monooxygenase gamma subunit
  • Ligand: COPPER (II) ION
  • Ligand: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
  • Ligand: water

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Supramolecule #1: particulate methane monooxygenase in native membrane arrays

SupramoleculeName: particulate methane monooxygenase in native membrane arrays
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)

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Macromolecule #1: Particulate methane monooxygenase alpha subunit

MacromoleculeName: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 42.832887 KDa
SequenceString: HGEKSQAAFM RMRTIHWYDL SWSKEKVKIN ETVEIKGKFH VFEGWPETVD EPDVAFLNVG MPGPVFIRKE SYIGGQLVPR SVRLEIGKT YDFRVVLKAR RPGDWHVHTM MNVQGGGPII GPGKWITVEG SMSEFRNPVT TLTGQTVDLE NYNEGNTYFW H AFWFAIGV ...String:
HGEKSQAAFM RMRTIHWYDL SWSKEKVKIN ETVEIKGKFH VFEGWPETVD EPDVAFLNVG MPGPVFIRKE SYIGGQLVPR SVRLEIGKT YDFRVVLKAR RPGDWHVHTM MNVQGGGPII GPGKWITVEG SMSEFRNPVT TLTGQTVDLE NYNEGNTYFW H AFWFAIGV AWIGYWSRRP IFIPRLLMVD AGRADELVSA TDRKVAMGFL AATILIVVMA MSSANSKYPI TIPLQAGTMR GM KPLELPA PTVSVKVEDA TYRVPGRAMR MKLTITNHGN SPIRLGEFYT ASVRFLDSDV YKDTTGYPED LLAEDGLSVS DNS PLAPGE TRTVDVTASD AAWEVYRLSD IIYDPDSRFA GLLFFFDATG NRQVVQIDAP LIPSFM

UniProtKB: Particulate methane monooxygenase alpha subunit

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Macromolecule #2: Particulate methane monooxygenase gamma subunit

MacromoleculeName: Particulate methane monooxygenase gamma subunit / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 27.954148 KDa
SequenceString: EAPLLDKKWL TFALAIYTVF YLWVRWYEGV YGWSAGLDSF APEFETYWMN FLYTEIVLEI VTASILWGYL WKTRDRNLAA LTPREELRR NFTHLVWLVA YAWAIYWGAS YFTEQDGTWH QTIVRDTDFT PSHIIEFYLS YPIYIITGFA AFIYAKTRLP F FAKGISLP ...String:
EAPLLDKKWL TFALAIYTVF YLWVRWYEGV YGWSAGLDSF APEFETYWMN FLYTEIVLEI VTASILWGYL WKTRDRNLAA LTPREELRR NFTHLVWLVA YAWAIYWGAS YFTEQDGTWH QTIVRDTDFT PSHIIEFYLS YPIYIITGFA AFIYAKTRLP F FAKGISLP YLVLVVGPFM ILPNVGLNEW GHTFWFMEEL FVAPLHYGFV IFGWLALAVM GTLTQTFYSF AQGGLGQSLC E

UniProtKB: Ammonia monooxygenase/methane monooxygenase, subunit C family protein

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Macromolecule #3: Particulate methane monooxygenase beta subunit

MacromoleculeName: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 27.855434 KDa
SequenceString: SAVRSHAEAV QVSRTIDWMA LFVVFFVIVG SYHIHAMLTM GDWDFWSDWK DRRLWVTVTP IVLVTFPAAV QSYLWERYRL PWGATVCVL GLLLGEWINR YFNFWGWTYF PINFVFPASL VPGAIILDTV LMLSGSYLFT AIVGAMGWGL IFYPGNWPII A PLHVPVEY ...String:
SAVRSHAEAV QVSRTIDWMA LFVVFFVIVG SYHIHAMLTM GDWDFWSDWK DRRLWVTVTP IVLVTFPAAV QSYLWERYRL PWGATVCVL GLLLGEWINR YFNFWGWTYF PINFVFPASL VPGAIILDTV LMLSGSYLFT AIVGAMGWGL IFYPGNWPII A PLHVPVEY NGMLMSIADI QGYNYVRTGT PEYIRMVEKG TLRTFGKDVA PVSAFFSAFM SILIYFMWHF IGRWFSNERF LQ S

UniProtKB: Particulate methane monooxygenase beta subunit

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Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #5: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecan...

MacromoleculeName: (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate
type: ligand / ID: 5 / Number of copies: 171 / Formula: A1A0P
Molecular weightTheoretical: 703.97 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1699 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9cl2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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