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- PDB-9cl2: Particulate methane monooxygenase in washed native membranes -

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Basic information

Entry
Database: PDB / ID: 9cl2
TitleParticulate methane monooxygenase in washed native membranes
Components(Particulate methane monooxygenase ...) x 3
KeywordsOXIDOREDUCTASE / membrane protein / metalloenzyme / monooxygenase
Function / homology
Function and homology information


methane monooxygenase (particulate) / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / monooxygenase activity / metal ion binding / membrane
Similarity search - Function
Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / 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: 2.42 Å
AuthorsTucci, F.J. / Rosenzweig, A.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118035 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM105538 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F31ES034283 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structures of methane and ammonia monooxygenases in native membranes.
Authors: Frank J Tucci / Amy C Rosenzweig /
Abstract: Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining ...Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining chemical transformations of their metabolisms: the oxidations of methane to methanol by particulate methane monooxygenase (pMMO) and ammonia to hydroxylamine by ammonia monooxygenase (AMO), enzymes of prime interest for applications in mitigating climate change. However, investigations of these enzymes have been hindered by the need for disruptive detergent solubilization prior to structure determination, confounding studies of pMMO and precluding studies of AMO. Here, we overcome these challenges by using cryoEM to visualize pMMO and AMO directly in their native membrane arrays at 2.4 to 2.8 Å resolution. These structures reveal details of the copper centers, numerous bound lipids, and previously unobserved components, including identifiable and distinct supernumerary helices interacting with pMMO and AMO, suggesting a widespread role for these helices in copper membrane monooxygenases. Comparisons between these structures, their metallocofactors, and their unexpected protein-protein interactions highlight features that may govern activity or the formation of higher-order arrays in native membranes. The ability to obtain molecular insights within the native membrane will enable further understanding of these environmentally important enzymes.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Ba: Particulate methane monooxygenase gamma subunit
Ca: Particulate methane monooxygenase beta subunit
Aa: Particulate methane monooxygenase alpha subunit
Cb: Particulate methane monooxygenase beta subunit
Cc: Particulate methane monooxygenase beta subunit
Ab: Particulate methane monooxygenase alpha subunit
Ac: Particulate methane monooxygenase alpha subunit
Bb: Particulate methane monooxygenase gamma subunit
Bc: Particulate methane monooxygenase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,62675
Polymers295,9279
Non-polymers40,69866
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Particulate methane monooxygenase ... , 3 types, 9 molecules BaBbBcCaCbCcAaAbAc

#1: Protein Particulate methane monooxygenase gamma subunit / Methane monooxygenase / C subunit


Mass: 27954.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
References: UniProt: Q603F1, methane monooxygenase (soluble)
#2: 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.: 3 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
References: UniProt: Q607G3, methane monooxygenase (particulate)
#3: Protein Particulate methane monooxygenase alpha subunit


Mass: 42832.887 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus str. Bath (bacteria)
References: UniProt: G1UBD1

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Non-polymers , 3 types, 639 molecules

#4: 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.: 57 / Source method: obtained synthetically / Formula: C38H74NO8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: obtained synthetically / Formula: H2O

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Details

Has ligand of interestY
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 washed native membranes
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: vitreous ice
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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129495 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221433
ELECTRON MICROSCOPYf_angle_d0.53929246
ELECTRON MICROSCOPYf_dihedral_angle_d5.0572808
ELECTRON MICROSCOPYf_chiral_restr0.0423151
ELECTRON MICROSCOPYf_plane_restr0.0053614

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