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- EMDB-39540: Cryo-EM structure of hydroxylase in soluble methane monooxygenase... -

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Basic information

Entry
Database: EMDB / ID: EMD-39540
TitleCryo-EM structure of hydroxylase in soluble methane monooxygenase from Methylosinus sporium 5
Map data
Sample
  • Complex: Cryo-EM structure of soluble methane monooxygenase hydroxylase
    • Protein or peptide: Methane monooxygenase
    • Protein or peptide: Methane monooxygenase
    • Protein or peptide: Methane monooxygenase
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsSoluble methane monooxygenase / Hydroxylase / Oxidoreductase / Diiron active site
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
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 ...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
Similarity search - Component
Biological speciesMethylosinus sporium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsHwang Y / Ryu B / Pozharski E / Lee SJ
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2015M3D3A1A01064876 (C1 Gas Refinery) 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 DH / Hong HJ / Na JG / Song CG / Kang HG / Pozharski E / Lee SJ
History
DepositionMar 21, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39540.png

Downloads & links

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Map

FileDownload / File: emd_39540.map.gz / Format: CCP4 / Size: 10.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 128 pix.
= 108.544 Å		0.85 Å/pix.
x 129 pix.
= 109.392 Å		0.85 Å/pix.
x 165 pix.
= 139.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-3.0148625 - 4.6692114
Average (Standard dev.)0.029716397 (±0.46573827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin967895
Dimensions129165128
Spacing165129128
CellA: 139.92 Å / B: 109.392 Å / C: 108.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39540_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39540_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39540_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of soluble methane monooxygenase hydroxylase

EntireName: Cryo-EM structure of soluble methane monooxygenase hydroxylase
Components
  • Complex: Cryo-EM structure of soluble methane monooxygenase hydroxylase
    • Protein or peptide: Methane monooxygenase
    • Protein or peptide: Methane monooxygenase
    • Protein or peptide: Methane monooxygenase
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of soluble methane monooxygenase hydroxylase

SupramoleculeName: Cryo-EM structure of soluble methane monooxygenase hydroxylase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Methylosinus sporium (bacteria) / Strain: 5

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Macromolecule #1: Methane monooxygenase

MacromoleculeName: Methane monooxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methylosinus sporium (bacteria) / Strain: 5
Molecular weightTheoretical: 59.97923 KDa
SequenceString: MAISLATKAA TDALKVNRAP VGVEPQEVHK WLQSFNWDFK ENRTKYATKY HMANQTKEQF KVIAKEYARM EAAKDERQFG TLLDGLTRL GAGNKVHPRW GETMKVISNF LEVGEYNAIA ASAMLWDSAT AAEQKNGYLA QVLDEIRHTH QCAFINHYYS K HYHDPAGH ...String:
MAISLATKAA TDALKVNRAP VGVEPQEVHK WLQSFNWDFK ENRTKYATKY HMANQTKEQF KVIAKEYARM EAAKDERQFG TLLDGLTRL GAGNKVHPRW GETMKVISNF LEVGEYNAIA ASAMLWDSAT AAEQKNGYLA QVLDEIRHTH QCAFINHYYS K HYHDPAGH NDARRTRAIG PLWKGMKRVF ADGFISGDAV ECSVNLQLVG EACFTNPLIV AVTEWASANG DEITPTVFLS VE TDELRHM ANGYQTVVSI ANDPAAAKYL NTDLNNAFWT QQKYFTPALG YLFEYGSKFK VEPWVKTWNR WVYEDWGGIW IGR LGKYGV ESPRSLRDAK TDAYWAHHDL ALAAYALWPL GFARLALPDE EDQEWFEANY PGWADHYGKI YNEWKKLGYE DPKS GFIPY AWLLANGHDV YIDRVSQVPF IPSLAKGSGS LRVHEFNGKK HSLTDDWGER MWLSEPERYE CHNLFEQYEG RELSE VIAE GHGVRSDGKT LIAQPHVRGD NLWTLEDIKR AGCVFPNPLA KF

UniProtKB: Methane monooxygenase

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Macromolecule #2: Methane monooxygenase

MacromoleculeName: Methane monooxygenase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methylosinus sporium (bacteria) / Strain: 5
Molecular weightTheoretical: 45.239246 KDa
SequenceString: MSQPQSSQVT KRGLTDPERA AIIAAAVPDH ALDTQRKYHY FIQPRWKRLS EYEQLSCYAQ PNPDWIAGGL DWGDWTQKFH GGRPSWGNE STELRTTDWY RHRDPARRWH APYVKDKSEE ARYTQRFLAA YSSEGSIRTI DAYWRDEILN KYYGALLYNE Y GLFNAHSS ...String:
MSQPQSSQVT KRGLTDPERA AIIAAAVPDH ALDTQRKYHY FIQPRWKRLS EYEQLSCYAQ PNPDWIAGGL DWGDWTQKFH GGRPSWGNE STELRTTDWY RHRDPARRWH APYVKDKSEE ARYTQRFLAA YSSEGSIRTI DAYWRDEILN KYYGALLYNE Y GLFNAHSS VGRDCLSDTI RQSATFAGLD KVDNAQMIQM ERLFIAKLVP GFDASTDVPK KIWTTDPIYA GARGAVEEIW QG IQDWNEI LWAGHAVYDA TFGQFARREF FQRLATVYGD TLTPFFTAQS QTYFQTTRGA IEDLFVYCLA NDPEFGAHNR TFL NAWTEH YLARSVTALK DFVGIYAKVE KVAGATDRAG VSEALQRVFG DWKVDYADKI GFNIDVDQKV DAVLAGFKN

UniProtKB: Methane monooxygenase

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Macromolecule #3: Methane monooxygenase

MacromoleculeName: Methane monooxygenase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methylosinus sporium (bacteria) / Strain: 5
Molecular weightTheoretical: 19.379207 KDa
SequenceString:
MAKREPIHEN STRTEWEGKI AKLNSVDQAT KFIQDFRVAY SSPFRKSYDL DVDYQYIERK IEERLSVLKT EKLSVADLVT KATTGEDAA AVEAAWIAKM KAAESKYAAE RIHIEFRQLY KPPVLPVNVF LRTDAALGTI LMELRNTDYY ATPLEGLRKE R GVKVLHLQ A

UniProtKB: Methane monooxygenase

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Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 61 / 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: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10001 / Average electron dose: 65.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.8000000000000003 µm / Calibrated defocus min: 0.445 µm / Calibrated magnification: 58893 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4980770
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1mty

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 407859
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1mty


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: PHENIX (ver. 1.19.2_4158:)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8yrd:
Cryo-EM structure of hydroxylase in soluble methane monooxygenase from Methylosinus sporium 5

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