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- EMDB-24830: CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in... -

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Basic information

Entry
Database: EMDB / ID: EMD-24830
TitleCryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution
Map dataCryoEM structure of Methylotuvimicrobium alcaliphilum 20Z in a POPC nanodisc at 2.42 angstrom resolution
Sample
  • Complex: pMMO complex in a POPC nanodisc
    • Protein or peptide: Particulate methane monooxygenase, B subunit
    • Protein or peptide: Particulate methane monooxygenase, A subunit
    • Protein or peptide: Particulate methane monooxygenase, C subunit
  • Ligand: COPPER (II) ION
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: DECANE
  • Ligand: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate
  • Ligand: water
KeywordsComplex / OXIDOREDUCTASE
Function / homology
Function and homology information


methane monooxygenase (soluble) / : / : / membrane / metal ion binding
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
Particulate methane monooxygenase, C subunit / Particulate methane monooxygenase, A subunit / Particulate methane monooxygenase, B subunit
Similarity search - Component
Biological speciesMethylotuvimicrobium alcaliphilum 20Z (bacteria) / Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsKoo CW / 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: Science / Year: 2022
Title: Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer.
Authors: Christopher W Koo / Frank J Tucci / Yuan He / Amy C Rosenzweig /
Abstract: Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using ...Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.
History
DepositionSep 9, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24830.png

Downloads & links

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Map

FileDownload / File: emd_24830.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of Methylotuvimicrobium alcaliphilum 20Z in a POPC nanodisc at 2.42 angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.53 Å/pix.
x 384 pix.
= 201.6 Å		0.53 Å/pix.
x 384 pix.
= 201.6 Å		0.53 Å/pix.
x 384 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.525 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0272
Minimum - Maximum-0.051349774 - 0.13660431
Average (Standard dev.)0.00018533606 (±0.005857473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 201.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : pMMO complex in a POPC nanodisc

EntireName: pMMO complex in a POPC nanodisc
Components
  • Complex: pMMO complex in a POPC nanodisc
    • Protein or peptide: Particulate methane monooxygenase, B subunit
    • Protein or peptide: Particulate methane monooxygenase, A subunit
    • Protein or peptide: Particulate methane monooxygenase, C subunit
  • Ligand: COPPER (II) ION
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: DECANE
  • Ligand: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate
  • Ligand: water

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Supramolecule #1: pMMO complex in a POPC nanodisc

SupramoleculeName: pMMO complex in a POPC nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Methylotuvimicrobium alcaliphilum 20Z (bacteria)

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Macromolecule #1: Particulate methane monooxygenase, B subunit

MacromoleculeName: Particulate methane monooxygenase, B subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble)
Source (natural)Organism: Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
Molecular weightTheoretical: 45.602125 KDa
SequenceString: MKIIKDKVAK LSFVALLVTV TAAMFYTPTA SAHGEKSQAA FMRMRTIHWF DLNWSKDQVS VNETMSISGK FHVFAGWPET VDKPEVAFL NIGIPGPVFI RAGSWIGGQL VPRSVSLELG ETYEFKVLLK ARRPGDWHVH TMMNVQGGGP IIGPGKWVTI T GSMGDFKN ...String:
MKIIKDKVAK LSFVALLVTV TAAMFYTPTA SAHGEKSQAA FMRMRTIHWF DLNWSKDQVS VNETMSISGK FHVFAGWPET VDKPEVAFL NIGIPGPVFI RAGSWIGGQL VPRSVSLELG ETYEFKVLLK ARRPGDWHVH TMMNVQGGGP IIGPGKWVTI T GSMGDFKN PITTLTGETI DLETYALDGV YGWHLFWYLL GVAWMVYWCR KPVFIPRRIA VDAGKADSLI TPTDKKVGMA FA AGTLAIV AVSMGQANEK YPVTTPLQAG LMRGIKSLEL PQPTVSVKVV DASYRVPGRA MQMTLEITNN GDSAVRLAEF NTA SVRFLD ADVYEDDTNY PDDLLAEEGL SVSDNSPLAP GETRTVDVTA SDAAWEVYRL ADLIYDPDSR FAGLLFFIDE DGNR QMTMV DAPLIPTFI

UniProtKB: Particulate methane monooxygenase, B subunit

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Macromolecule #2: Particulate methane monooxygenase, A subunit

MacromoleculeName: Particulate methane monooxygenase, A subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble)
Source (natural)Organism: Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
Molecular weightTheoretical: 28.277934 KDa
SequenceString: MSASQSAVRS RAEAVKVSRT FDYMILFTVF FVVLGGYHIH YMLTGGDWDF WTDWKDRRLW VTVAPIVSIT FPAAVQAVLW WRYRIAWGA TLCVLGLLLG EWINRYFNFW GWTYFPVNFV FPSNLMPGAI VLDVILMLSN SMTLTAVVGG LAWGLLFYPG N WPIIAPLH ...String:
MSASQSAVRS RAEAVKVSRT FDYMILFTVF FVVLGGYHIH YMLTGGDWDF WTDWKDRRLW VTVAPIVSIT FPAAVQAVLW WRYRIAWGA TLCVLGLLLG EWINRYFNFW GWTYFPVNFV FPSNLMPGAI VLDVILMLSN SMTLTAVVGG LAWGLLFYPG N WPIIAPLH VPVEYNGMMM TLADLQGYHY VRTGTPEYIR MVEKGTLRTF GKDVAPVSAF FSGFVSILIY FLWHFFGSWF GS EKFVQAA

UniProtKB: Particulate methane monooxygenase, A subunit

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Macromolecule #3: Particulate methane monooxygenase, C subunit

MacromoleculeName: Particulate methane monooxygenase, C subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble)
Source (natural)Organism: Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
Molecular weightTheoretical: 28.872328 KDa
SequenceString: MAATTESVKA DAAEAPLLNK KNIIAGASLY LVFYAWVRWY EGVYGWSAGL DSFAPEFETY WMNFLYIEMV LEVLVASVLW GYIWKSRDR KVMSITPREE LRRHFTHWTW LMMYGIAIYF GASYFTEQDG TWHQTIVRDT DFTPSHIIEF YLSYPIYIIT G GASFLYAK ...String:
MAATTESVKA DAAEAPLLNK KNIIAGASLY LVFYAWVRWY EGVYGWSAGL DSFAPEFETY WMNFLYIEMV LEVLVASVLW GYIWKSRDR KVMSITPREE LRRHFTHWTW LMMYGIAIYF GASYFTEQDG TWHQTIVRDT DFTPSHIIEF YLSYPIYIIT G GASFLYAK TRLPTYQQGL SLQYLVVVVG PFMILPNVGL NEWGHTFWFM EELFVAPLHY GFVFFGWSAL GVLGVINIEL GA LSKLLKK DLA

UniProtKB: Particulate methane monooxygenase, C subunit

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Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 9 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #5: 1,2-dihexanoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1,2-dihexanoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 15 / Formula: HXG
Molecular weightTheoretical: 454.515 Da
Chemical component information

ChemComp-HXG:
1,2-dihexanoyl-sn-glycero-3-phosphocholine

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Macromolecule #6: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 6 / Number of copies: 9 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #7: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate

MacromoleculeName: (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate
type: ligand / ID: 7 / Number of copies: 3 / Formula: 6ER
Molecular weightTheoretical: 454.515 Da
Chemical component information

ChemComp-6ER:
(S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 3 / 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 stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 443800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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