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- PDB-8xiw: Cryo-EM complex structure between hydroxylase and regulatory comp... -

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Basic information

Entry
Database: PDB / ID: 8xiw
TitleCryo-EM complex structure between hydroxylase and regulatory component from soluble methane monooxygenase
Components(Methane monooxygenase) x 4
KeywordsOXIDOREDUCTASE / soluble methane monooxygenase / hydroxylase / regulatory component
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase [NAD(P)H] activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : ...: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Methane monooxygenase / Methane monooxygenase / Methane monooxygenase / Methane monooxygenase
Similarity search - Component
Biological speciesMethylosinus sporium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsHwang, Y. / Ryu, B. / Pozharski, E. / Lee, S.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2015M3D3A1A01064876 Korea, Republic Of
Ministry of Education (MoE, Korea)2017R1A6A1A03015876 Korea, Republic Of
CitationJournal: Biorxiv / Year: 2025
Title: Heartbeat-like dynamics drives oxygen activation in methane monooxygenase
Authors: Hwang, Y. / Ryu, B. / Lee, D.H. / Hong, H.J. / Na, J.G. / Song, C.G. / Kang, H.G. / Pozharski, E. / Lee, S.J.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methane monooxygenase
B: Methane monooxygenase
C: Methane monooxygenase
D: Methane monooxygenase
E: Methane monooxygenase
F: Methane monooxygenase
G: Methane monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,33611
Polymers264,1127
Non-polymers2234
Water1,69394
1


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

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Components

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Protein , 4 types, 7 molecules AEBFCGD

#1: Protein Methane monooxygenase / MmoX1 / Alpha-subunit


Mass: 59979.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN7
#2: Protein Methane monooxygenase / MmoY / Beta-subunit


Mass: 45239.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN6
#3: Protein Methane monooxygenase / MmoZ / Gamma-subunit


Mass: 19379.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN4
#4: Protein Methane monooxygenase / MmoB


Mass: 14916.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus sporium (bacteria) / Gene: mmoB, C5689_05360, FM996_19905 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27RN5

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Non-polymers , 2 types, 98 molecules

#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: Cryo-EM structure of soluble methane monooxygenase hydroxylase in complex with regulatory subunit
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methylosinus sporium (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 58893 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Calibrated defocus min: 445 nm / Calibrated defocus max: 3800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage exposure time: 5.24 sec. / Electron dose: 58.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9471
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
2cryoSPARC3.3.1image acquisition
4cryoSPARC3.1.1CTF correction
7PHENIX1.19.2-4158model fitting
9cryoSPARC3.1.1initial Euler assignment
10cryoSPARC3.1.1final Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.19.2-4158model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5970601
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200043 / Algorithm: FOURIER SPACE / Num. of class averages: 15 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4GAM

4gam


Accession code: 4GAM / Source name: PDB / Type: experimental model

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