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- EMDB-45662: particulate methane monooxygenase in native membranes -

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Basic information

Entry
Database: EMDB / ID: EMD-45662
Titleparticulate methane monooxygenase in native membranes
Map data
Sample
  • Organelle or cellular component: particulate methane monooxygenase in native membranes from Methylocystis sp. ATCC 49242
    • Protein or peptide: Methane monooxygenase/ammonia monooxygenase subunit A
    • Protein or peptide: Methane monooxygenase/ammonia monooxygenase subunit B
    • Protein or peptide: Particulate methane monooxygenase subunit C
    • Protein or peptide: particulate methane monooxygenase supernumerary helix
  • Ligand: COPPER (II) ION
  • Ligand: water
Keywordsmembrane protein / metalloenzyme / monooxygenase / OXIDOREDUCTASE
Function / homology
Function and homology information


monooxygenase activity / 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
Methane monooxygenase/ammonia monooxygenase subunit B / Methane monooxygenase/ammonia monooxygenase subunit A / Particulate methane monooxygenase subunit C
Similarity search - Component
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsTucci FJ / Rosenzweig AC
Funding support United States, 3 items
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, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45662.png

Downloads & links

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Map

FileDownload / File: emd_45662.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.179
Minimum - Maximum-0.50772166 - 0.9209995
Average (Standard dev.)0.0014685786 (±0.029787032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45662_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45662_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : particulate methane monooxygenase in native membranes from Methyl...

EntireName: particulate methane monooxygenase in native membranes from Methylocystis sp. ATCC 49242
Components
  • Organelle or cellular component: particulate methane monooxygenase in native membranes from Methylocystis sp. ATCC 49242
    • Protein or peptide: Methane monooxygenase/ammonia monooxygenase subunit A
    • Protein or peptide: Methane monooxygenase/ammonia monooxygenase subunit B
    • Protein or peptide: Particulate methane monooxygenase subunit C
    • Protein or peptide: particulate methane monooxygenase supernumerary helix
  • Ligand: COPPER (II) ION
  • Ligand: water

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Supramolecule #1: particulate methane monooxygenase in native membranes from Methyl...

SupramoleculeName: particulate methane monooxygenase in native membranes from Methylocystis sp. ATCC 49242
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)

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Macromolecule #1: Methane monooxygenase/ammonia monooxygenase subunit A

MacromoleculeName: Methane monooxygenase/ammonia monooxygenase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)
Molecular weightTheoretical: 27.796467 KDa
SequenceString: AVGPFNSVAE AAGCVQTVDW MLLVLLFFAV LGGYHVHFML TAGDWDFWVD WKDRRMWPTV VPILGVTFCA ASQAFWWVNF RLPFGAVFA ALGLLIGEWI NRYVNFWGWT YFPISLVFPS ALIVPAIWLD VILLLSGSYV ITAVVGSLGW GLLFYPNNWP A IAAFHQAT ...String:
AVGPFNSVAE AAGCVQTVDW MLLVLLFFAV LGGYHVHFML TAGDWDFWVD WKDRRMWPTV VPILGVTFCA ASQAFWWVNF RLPFGAVFA ALGLLIGEWI NRYVNFWGWT YFPISLVFPS ALIVPAIWLD VILLLSGSYV ITAVVGSLGW GLLFYPNNWP A IAAFHQAT EQHGQLMTLA DLIGFHFVRT SMPEYIRMVE RGTLRTFGKD VVPVAAFFSG FVSMMVYFLW WFMGRWYSTT KV IDTI

UniProtKB: Methane monooxygenase/ammonia monooxygenase subunit A

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Macromolecule #2: Methane monooxygenase/ammonia monooxygenase subunit B

MacromoleculeName: Methane monooxygenase/ammonia monooxygenase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)
Molecular weightTheoretical: 42.785566 KDa
SequenceString: HGEKSQQAFL RMRTLNWYDV QWSKTTVNVN EEMVLSGKVH VFSAWPQAVA NPRVSFLNAG EPGPVLVRTA QFIGEQFAPR SVSLEIGKD YAFSINLRGR RAGRWHVHAQ INVEGGGPII GPGQWIEIKG DMKDFTDPVT LLDGSTVDLE HYGISRVYAW H LPWMAVGA ...String:
HGEKSQQAFL RMRTLNWYDV QWSKTTVNVN EEMVLSGKVH VFSAWPQAVA NPRVSFLNAG EPGPVLVRTA QFIGEQFAPR SVSLEIGKD YAFSINLRGR RAGRWHVHAQ INVEGGGPII GPGQWIEIKG DMKDFTDPVT LLDGSTVDLE HYGISRVYAW H LPWMAVGA AWIFFWFVRK GIITSYIRVA EGKADDVIGD DDRRIGAIVL ALTILATIVG YAVTNSTFPR TIPLQAGLQK PL TPIETEG TVGVGKENVT TELNGGVYKV PGRELTINVK VKNNTSQPLR LGEYTAAGLR FLNPDVFTTK PDFPDYLLAD RGL SVDATP IAPGEAKEIV VKIQDARWDI ERLSDLAYDT DSQIGGLLFF FSPDGKRYAS EIGGPVIPKF VA

UniProtKB: Methane monooxygenase/ammonia monooxygenase subunit B

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Macromolecule #3: Particulate methane monooxygenase subunit C

MacromoleculeName: Particulate methane monooxygenase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)
Molecular weightTheoretical: 27.924629 KDa
SequenceString: ESVVDLRGMW IGLVLLNVFY LIVRIYEQVF GWRAGLDSFA PEFQTYWMSI LWTEIPLELV SGLGLAGYLW KTRDRNVDAV TPREEMRRL VVLVQWLVVY GIAIYWGASF FTEQDGTWHM TVIRDTDFTP SHIIEFYMSY PIYSVIAVGA FFYAKTRIPY F AHGYSLAF ...String:
ESVVDLRGMW IGLVLLNVFY LIVRIYEQVF GWRAGLDSFA PEFQTYWMSI LWTEIPLELV SGLGLAGYLW KTRDRNVDAV TPREEMRRL VVLVQWLVVY GIAIYWGASF FTEQDGTWHM TVIRDTDFTP SHIIEFYMSY PIYSVIAVGA FFYAKTRIPY F AHGYSLAF LIVAIGPFMI IPNVGLNEWG HTFWFMEELF VAPLHWGFVF FGWMALGVFG VVLQILMRIH ALVGKEGVKL LT E

UniProtKB: Particulate methane monooxygenase subunit C

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Macromolecule #4: particulate methane monooxygenase supernumerary helix

MacromoleculeName: particulate methane monooxygenase supernumerary helix / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)
Molecular weightTheoretical: 2.429082 KDa
SequenceString:
MGWLVPAAML AMVVIAAVTL TRL

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Macromolecule #5: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 819 / 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

BufferpH: 7.3
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7s4m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160646
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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