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- EMDB-62776: Cryo-EM structure of soluble methane monooxygenase hydroxylase fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-62776
TitleCryo-EM structure of soluble methane monooxygenase hydroxylase 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 monoxoygenase / hydroxylase / homodimer / OXIDOREDUCTASE
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: 3.42 Å
AuthorsHwang Y / Pozharski E / Lee SJ
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2023RIS-008 Korea, Republic Of
Ministry of Education (MoE, Korea)2017R1A6A1A03015876 Korea, Republic Of
CitationJournal: To be published
Title: Complex formation via regulatory component of MMOH from Methylosinus sporium 5
Authors: Hwang Y / Pozharski E / Lee SJ
History
DepositionDec 17, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62776.png

Downloads & links

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Map

FileDownload / File: emd_62776.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.52 Å		0.86 Å/pix.
x 320 pix.
= 275.52 Å		0.86 Å/pix.
x 320 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.52433205 - 1.3582531
Average (Standard dev.)0.0011993832 (±0.051072378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62776_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62776_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62776_half_map_2.map
Projections & Slices
AxesZYX

Projections

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)

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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)
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)
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)
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: 6 / 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

Concentration2.0 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 36.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 120000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 374590
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1mty

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 60960
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 10 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9l2i:
Cryo-EM structure of soluble methane monooxygenase hydroxylase from Methylosinus sporium 5

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