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- EMDB-24831: CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POP... -

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Basic information

Entry
Database: EMDB / ID: EMD-24831
TitleCryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at 2.42 Angstrom resolution
Map dataCryoEM structure of Methylocystis species strain Rockwell pMMO in a POPC nanodisc at 2.42 angstrom resolution
Sample
  • Complex: pMMO complex in a native lipid nanodisc
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
    • Protein or peptide: Unidentified Helix
  • Ligand: COPPER (II) ION
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: water
KeywordsComplex / OXIDOREDUCTASE
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 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_24831.png

Downloads & links

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Map

FileDownload / File: emd_24831.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of Methylocystis species strain Rockwell pMMO in a POPC nanodisc at 2.42 angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.52 Å/pix.
x 384 pix.
= 199.68 Å		0.52 Å/pix.
x 384 pix.
= 199.68 Å		0.52 Å/pix.
x 384 pix.
= 199.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0758
Minimum - Maximum-0.33880538 - 0.4193564
Average (Standard dev.)0.00042710776 (±0.020475218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 199.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM structure of Methylocystis species strain Rockwell pMMO...

Fileemd_24831_additional_1.map
AnnotationCryoEM structure of Methylocystis species strain Rockwell pMMO in a POPC nanodisc at 2.42 angstrom resolution processed by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pMMO complex in a native lipid nanodisc

EntireName: pMMO complex in a native lipid nanodisc
Components
  • Complex: pMMO complex in a native lipid nanodisc
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Particulate methane monooxygenase beta subunit
    • Protein or peptide: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
    • Protein or peptide: Unidentified Helix
  • Ligand: COPPER (II) ION
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: water

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Supramolecule #1: pMMO complex in a native lipid nanodisc

SupramoleculeName: pMMO complex in a native lipid nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)

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Macromolecule #1: Particulate methane monooxygenase alpha subunit

MacromoleculeName: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: Particulate methane monooxygenase beta subunit

MacromoleculeName: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Ammonia monooxygenase/methane monooxygenase, subunit C family protein

MacromoleculeName: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
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

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Macromolecule #4: Unidentified Helix

MacromoleculeName: Unidentified Helix / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Methylocystis sp. ATCC 49242 (bacteria)
Molecular weightTheoretical: 1.635006 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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

MacromoleculeName: 1,2-dihexanoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 6 / Number of copies: 12 / Formula: HXG
Molecular weightTheoretical: 454.515 Da
Chemical component information

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

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Macromolecule #7: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 7 / Number of copies: 6 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #8: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 8 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 36 / 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: 1.02 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: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 490196
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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