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- EMDB-45663: Ammonia monooxygenase in native membranes -

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Basic information

Entry
Database: EMDB / ID: EMD-45663
TitleAmmonia monooxygenase in native membranes
Map data
Sample
  • Organelle or cellular component: ammonia monooxygenase in native membranes
    • Protein or peptide: Ammonia monooxygenase subunit C
    • Protein or peptide: Ammonia monooxygenase beta subunit
    • Protein or peptide: Ammonia monooxygenase alpha subunit
    • Protein or peptide: ammonia monooxygenase supernumerary helix
  • Ligand: COPPER (II) ION
  • Ligand: water
Keywordsmembrane protein / metalloenzyme / monooxygenase / OXIDOREDUCTASE
Function / homology
Function and homology information


ammonia monooxygenase / ammonia monooxygenase activity / monooxygenase activity / metal ion binding / membrane / plasma membrane / cytoplasm
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
Ammonia monooxygenase alpha subunit / Ammonia monooxygenase beta subunit / Ammonia monooxygenase subunit C
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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_45663.png

Downloads & links

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Map

FileDownload / File: emd_45663.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.775
Minimum - Maximum-4.704293 - 6.387256
Average (Standard dev.)0.006158166 (±0.19344147)
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_45663_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45663_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : ammonia monooxygenase in native membranes

EntireName: ammonia monooxygenase in native membranes
Components
  • Organelle or cellular component: ammonia monooxygenase in native membranes
    • Protein or peptide: Ammonia monooxygenase subunit C
    • Protein or peptide: Ammonia monooxygenase beta subunit
    • Protein or peptide: Ammonia monooxygenase alpha subunit
    • Protein or peptide: ammonia monooxygenase supernumerary helix
  • Ligand: COPPER (II) ION
  • Ligand: water

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Supramolecule #1: ammonia monooxygenase in native membranes

SupramoleculeName: ammonia monooxygenase in native membranes / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Nitrosomonas europaea ATCC 19718 (bacteria)

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Macromolecule #1: Ammonia monooxygenase subunit C

MacromoleculeName: Ammonia monooxygenase subunit C / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nitrosomonas europaea ATCC 19718 (bacteria)
Molecular weightTheoretical: 29.956896 KDa
SequenceString: YDMSLWYDSK FYKFGMITML LVAIFWVWYQ RYFAYSHGMD SMEPEFDRVW MGLWRVHMAI MPLFALVTWG WILKTRDTKE QLDNLDPKL EIKRYFYYMM WLGVYIFGVY WGGSFFTEQD ASWHQVIIRD TSFTPSHVVM FYGSFPMYIV CGVATYLYAM T RLPLFSRG ...String:
YDMSLWYDSK FYKFGMITML LVAIFWVWYQ RYFAYSHGMD SMEPEFDRVW MGLWRVHMAI MPLFALVTWG WILKTRDTKE QLDNLDPKL EIKRYFYYMM WLGVYIFGVY WGGSFFTEQD ASWHQVIIRD TSFTPSHVVM FYGSFPMYIV CGVATYLYAM T RLPLFSRG ISFPLVMAIA GPLMILPNVG LNEWGHAFWF MEELFSAPLH WGFVVLGWAG LFQGGVAAQI ITRYSNLTDV VW NNQSKEI LNNRIVA

UniProtKB: Ammonia monooxygenase subunit C

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Macromolecule #2: Ammonia monooxygenase beta subunit

MacromoleculeName: Ammonia monooxygenase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: ammonia monooxygenase
Source (natural)Organism: Nitrosomonas europaea ATCC 19718 (bacteria)
Molecular weightTheoretical: 43.037168 KDa
SequenceString: HGERSQEPFL RMRTVQWYDI KWGPEVTKVN ENAKITGKFH LAEDWPRAAA QPDFSFFNVG SPSPVFVRLS TKINGHPWFI SGPLQIGRD YEFEVNLRAR IPGRHHMHAM LNVKDAGPIA GPGAWMNITG SWDDFTNPLK LLTGETIDSE TFNLSNGIFW H VVWMSIGI ...String:
HGERSQEPFL RMRTVQWYDI KWGPEVTKVN ENAKITGKFH LAEDWPRAAA QPDFSFFNVG SPSPVFVRLS TKINGHPWFI SGPLQIGRD YEFEVNLRAR IPGRHHMHAM LNVKDAGPIA GPGAWMNITG SWDDFTNPLK LLTGETIDSE TFNLSNGIFW H VVWMSIGI FWIGVFTARP MFLPRSRVLL AYGDDLLMDP MDKKITWVLA ILTLALVWGG YRYTENKHPY TVPIQAGQSK VA ALPVAPN PVSIVITDAN YDVPGRALRV TMEVTNNGDI PVTFGEFTTA GIRFINSTGR KYLDPQYPRE LIAVGLNFDD ESA IQPGQT KELKMEAKDA LWEIQRLMAL LGDPESRFGG LLMSWDAEGN RHINSIAGPV IPVFTKL

UniProtKB: Ammonia monooxygenase beta subunit

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Macromolecule #3: Ammonia monooxygenase alpha subunit

MacromoleculeName: Ammonia monooxygenase alpha subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: ammonia monooxygenase
Source (natural)Organism: Nitrosomonas europaea ATCC 19718 (bacteria)
Molecular weightTheoretical: 31.800271 KDa
SequenceString: IFRTEEILKA AKMPPEAVHM SRLIDAVYFP ILIILLVGTY HMHFMLLAGD WDFWMDWKDR QWWPVVTPIV GITYCSAIMY YLWVNYRQP FGATLCVVCL LIGEWLTRYW GFYWWSHYPI NFVTPGIMLP GALMLDFTLY LTRNWLVTAL VGGGFFGLLF Y PGNWPIFG ...String:
IFRTEEILKA AKMPPEAVHM SRLIDAVYFP ILIILLVGTY HMHFMLLAGD WDFWMDWKDR QWWPVVTPIV GITYCSAIMY YLWVNYRQP FGATLCVVCL LIGEWLTRYW GFYWWSHYPI NFVTPGIMLP GALMLDFTLY LTRNWLVTAL VGGGFFGLLF Y PGNWPIFG PTHLPIVVEG TLLSMADYMG HLYVRTGTPE YVRHIEQGSL RTFGGHTTVI AAFFSAFVSM LMFTVWWYLG KV YCTAFFY VKGKRGRIVH RNDVTAFGEE GFPEGIK

UniProtKB: Ammonia monooxygenase alpha subunit

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Macromolecule #4: ammonia monooxygenase supernumerary helix

MacromoleculeName: ammonia monooxygenase supernumerary helix / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nitrosomonas europaea ATCC 19718 (bacteria)
Molecular weightTheoretical: 4.10773 KDa
SequenceString:
DAATTQREIE KNSGAWKVIL VSTAAFIVIG AIIWFGGIG

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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: 822 / 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
Sugar embeddingMaterial: vitreous ice
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
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: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79436
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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