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- PDB-11ll: Particulate methane monooxygenase in membrane arrays -

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Basic information

Entry
Database: PDB / ID: 11ll
TitleParticulate methane monooxygenase in membrane arrays
Components(Particulate methane monooxygenase ...) x 3
KeywordsOXIDOREDUCTASE / particulate methane monooxygenase
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
: / COPPER (II) ION / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsTucci, F.J. / Miller, C.G. / Rosenzweig, A.C.
Funding support United States, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Aa: Particulate methane monooxygenase alpha subunit
Ab: Particulate methane monooxygenase alpha subunit
Ac: Particulate methane monooxygenase alpha subunit
Ad: Particulate methane monooxygenase alpha subunit
Ae: Particulate methane monooxygenase alpha subunit
Af: Particulate methane monooxygenase alpha subunit
Ag: Particulate methane monooxygenase alpha subunit
Ah: Particulate methane monooxygenase alpha subunit
Ai: Particulate methane monooxygenase alpha subunit
Ba: Particulate methane monooxygenase gamma subunit
Bb: Particulate methane monooxygenase gamma subunit
Bc: Particulate methane monooxygenase gamma subunit
Bd: Particulate methane monooxygenase gamma subunit
Be: Particulate methane monooxygenase gamma subunit
Bf: Particulate methane monooxygenase gamma subunit
Bg: Particulate methane monooxygenase gamma subunit
Bh: Particulate methane monooxygenase gamma subunit
Bi: Particulate methane monooxygenase gamma subunit
Ca: Particulate methane monooxygenase beta subunit
Cb: Particulate methane monooxygenase beta subunit
Cc: Particulate methane monooxygenase beta subunit
Cd: Particulate methane monooxygenase beta subunit
Ce: Particulate methane monooxygenase beta subunit
Cf: Particulate methane monooxygenase beta subunit
Cg: Particulate methane monooxygenase beta subunit
Ch: Particulate methane monooxygenase beta subunit
Ci: Particulate methane monooxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,008,924210
Polymers887,78227
Non-polymers121,141183
Water30,6071699
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Particulate methane monooxygenase ... , 3 types, 27 molecules AaAbAcAdAeAfAgAhAiBaBbBcBdBeBfBgBhBiCaCbCcCdCeCfCgChCi

#1: Protein
Particulate methane monooxygenase alpha subunit


Mass: 42832.887 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
References: UniProt: G1UBD1
#2: Protein
Particulate methane monooxygenase gamma subunit / Methane monooxygenase / C subunit


Mass: 27954.148 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
References: UniProt: Q603F1, methane monooxygenase (soluble)
#3: Protein
Particulate methane monooxygenase beta subunit / Methane monooxygenase A subunit / Particulate methane monooxygenase 27 kDa subunit / Particulate ...Methane monooxygenase A subunit / Particulate methane monooxygenase 27 kDa subunit / Particulate methane monooxygenase hydroxylase 26 kDa subunit / Particulate methane monooxygenase hydroxylase beta subunit / pMMO-H beta subunit


Mass: 27855.434 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
References: UniProt: Q607G3, methane monooxygenase (particulate)

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Non-polymers , 3 types, 1882 molecules

#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#5: Chemical...
ChemComp-A1A0P / (2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexadecanoyloxy)propyl (9Z)-heptadec-9-enoate


Mass: 703.970 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: C38H74NO8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1699 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: particulate methane monooxygenase in native membrane arrays
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1, #3, #2 / Source: NATURAL
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Buffer solutionpH: 7.2
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2UCSF ChimeraX1.10/v10model fitting
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35000 / Symmetry type: POINT

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