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- PDB-7s4l: CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in... -

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Basic information

Entry
Database: PDB / ID: 7s4l
TitleCryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution
Components(Particulate methane monooxygenase, ...) x 3
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] 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
Chem-6ER / COPPER (II) ION / DECANE / 1,2-dihexanoyl-sn-glycero-3-phosphocholine / Particulate methane monooxygenase, C subunit / Particulate methane monooxygenase, A subunit / Particulate methane monooxygenase, B subunit
Similarity search - Component
Biological speciesMethylomicrobium alcaliphilum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsKoo, C.W. / Rosenzweig, A.C.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Particulate methane monooxygenase, B subunit
B: Particulate methane monooxygenase, A subunit
C: Particulate methane monooxygenase, C subunit
H: Particulate methane monooxygenase, C subunit
I: Particulate methane monooxygenase, C subunit
F: Particulate methane monooxygenase, A subunit
G: Particulate methane monooxygenase, A subunit
D: Particulate methane monooxygenase, B subunit
E: Particulate methane monooxygenase, B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,29145
Polymers308,2579
Non-polymers10,03436
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein Particulate methane monooxygenase, B subunit


Mass: 45602.125 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ64, methane monooxygenase (soluble)
#2: Protein Particulate methane monooxygenase, A subunit


Mass: 28277.934 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ63, methane monooxygenase (soluble)
#3: Protein Particulate methane monooxygenase, C subunit


Mass: 28872.328 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ62, methane monooxygenase (soluble)

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Non-polymers , 5 types, 39 molecules

#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-HXG / 1,2-dihexanoyl-sn-glycero-3-phosphocholine / (4R,7R)-7-(hexanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphapentadecan-1-aminium 4-oxide


Mass: 454.515 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C20H41NO8P
#6: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22
#7: Chemical ChemComp-6ER / (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio)ethyl)phosphate


Mass: 454.515 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H41NO8P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: pMMO complex in a POPC nanodisc / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methylotuvimicrobium alcaliphilum 20Z (bacteria)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443800 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00721492
ELECTRON MICROSCOPYf_angle_d0.70929310
ELECTRON MICROSCOPYf_dihedral_angle_d22.9892910
ELECTRON MICROSCOPYf_chiral_restr0.0473144
ELECTRON MICROSCOPYf_plane_restr0.0043612

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