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- PDB-7s4m: CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POP... -

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Basic information

Entry
Database: PDB / ID: 7s4m
TitleCryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at 2.42 Angstrom resolution
Components
  • (Particulate methane monooxygenase ...Methane monooxygenase (particulate)) x 2
  • Ammonia monooxygenase/methane monooxygenase, subunit C family protein
  • Unidentified Helix
KeywordsOXIDOREDUCTASE / Complex
Function / homologyCOPPER (II) ION / DECANE / DODECANE / 1,2-dihexanoyl-sn-glycero-3-phosphocholine
Function and homology information
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 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 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Particulate methane monooxygenase alpha subunit
F: Particulate methane monooxygenase beta subunit
B: Particulate methane monooxygenase beta subunit
J: Particulate methane monooxygenase beta subunit
G: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
C: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
D: Unidentified Helix
K: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
N: Unidentified Helix
H: Unidentified Helix
E: Particulate methane monooxygenase alpha subunit
I: Particulate methane monooxygenase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,62539
Polymers300,42512
Non-polymers7,20027
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Particulate methane monooxygenase ... , 2 types, 6 molecules AEIFBJ

#1: Protein Particulate methane monooxygenase alpha subunit


Mass: 42785.566 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)
#2: Protein Particulate methane monooxygenase beta subunit


Mass: 27796.467 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)

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Protein / Protein/peptide , 2 types, 6 molecules GCKDNH

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


Mass: 27924.629 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)
#4: Protein/peptide Unidentified Helix


Mass: 1635.006 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Methylocystis sp. ATCC 49242 (bacteria)

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Non-polymers , 5 types, 63 molecules

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


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: 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.: 12 / Source method: isolated from a natural source / Formula: C20H41NO8P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 native lipid nanodisc / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Methylocystis sp. ATCC 49242 (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 FIELDBright-field microscopy
Image recordingElectron dose: 1.02 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490196 / Symmetry type: POINT

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