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- EMDB-40718: particulate methane monooxygenase incubated with 4,4,4-trifluorob... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-40718
Titleparticulate methane monooxygenase incubated with 4,4,4-trifluorobutanol
Map data
Sample
  • Complex: particulate methane monooxygenase
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
  • Protein or peptide: Particulate methane monooxygenase beta subunit
  • Ligand: COPPER (II) ION
  • Ligand: DECANE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: water
Keywordsmetalloenzyme / membrane protein / nanodiscs / oxidoreductase
Function / homology
Function and homology information


methane monooxygenase (particulate) / methane monooxygenase (soluble) / : / : / monooxygenase activity / membrane / metal ion binding
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
Particulate methane monooxygenase alpha subunit / Ammonia monooxygenase/methane monooxygenase, subunit C family protein / Particulate methane monooxygenase beta subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsTucci FJ / Rosenzweig AC / Hoffman BM
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118035 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111097 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM105538 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F31ES034283 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008382 United States
National Science Foundation (NSF, United States)MCB-1908587 United States
CitationJournal: Nat Catal / Year: 2023
Title: Product analogue binding identifies the copper active site of particulate methane monooyxgenase
Authors: Tucci FJ / Jodts RJ / Hoffman BM / Rosenzweig AC
History
DepositionMay 5, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40718.png

Downloads & links

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Map

FileDownload / File: emd_40718.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 512 pix.
= 273.715 Å		0.53 Å/pix.
x 512 pix.
= 273.715 Å		0.53 Å/pix.
x 512 pix.
= 273.715 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5346 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.69881964 - 0.90254
Average (Standard dev.)0.0013756797 (±0.021956375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 273.7152 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40718_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_40718_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 : particulate methane monooxygenase

EntireName: particulate methane monooxygenase
Components
  • Complex: particulate methane monooxygenase
    • Protein or peptide: Particulate methane monooxygenase alpha subunit
    • Protein or peptide: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
  • Protein or peptide: Particulate methane monooxygenase beta subunit
  • Ligand: COPPER (II) ION
  • Ligand: DECANE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-dihexanoyl-sn-glycero-3-phosphocholine
  • Ligand: water

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Supramolecule #1: particulate methane monooxygenase

SupramoleculeName: particulate methane monooxygenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria)
Molecular weightTheoretical: 337.11 kDa/nm

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Macromolecule #1: Particulate methane monooxygenase alpha subunit

MacromoleculeName: Particulate methane monooxygenase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria) / Strain: Bath
Molecular weightTheoretical: 46.129746 KDa
SequenceString: MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN ...String:
MKTIKDRIAK WSAIGLLSAV AATAFYAPSA SAHGEKSQAA FMRMRTIHWY DLSWSKEKVK INETVEIKGK FHVFEGWPET VDEPDVAFL NVGMPGPVFI RKESYIGGQL VPRSVRLEIG KTYDFRVVLK ARRPGDWHVH TMMNVQGGGP IIGPGKWITV E GSMSEFRN PVTTLTGQTV DLENYNEGNT YFWHAFWFAI GVAWIGYWSR RPIFIPRLLM VDAGRADELV SATDRKVAMG FL AATILIV VMAMSSANSK YPITIPLQAG TMRGMKPLEL PAPTVSVKVE DATYRVPGRA MRMKLTITNH GNSPIRLGEF YTA SVRFLD SDVYKDTTGY PEDLLAEDGL SVSDNSPLAP GETRTVDVTA SDAAWEVYRL SDIIYDPDSR FAGLLFFFDA TGNR QVVQI DAPLIPSFM

UniProtKB: Particulate methane monooxygenase alpha subunit

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Macromolecule #2: Particulate methane monooxygenase beta subunit

MacromoleculeName: Particulate methane monooxygenase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (particulate)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria) / Strain: Bath
Molecular weightTheoretical: 28.445098 KDa
SequenceString: MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH ...String:
MSAAQSAVRS HAEAVQVSRT IDWMALFVVF FVIVGSYHIH AMLTMGDWDF WSDWKDRRLW VTVTPIVLVT FPAAVQSYLW ERYRLPWGA TVCVLGLLLG EWINRYFNFW GWTYFPINFV FPASLVPGAI ILDTVLMLSG SYLFTAIVGA MGWGLIFYPG N WPIIAPLH VPVEYNGMLM SIADIQGYNY VRTGTPEYIR MVEKGTLRTF GKDVAPVSAF FSAFMSILIY FMWHFIGRWF SN ERFLQST

UniProtKB: Particulate methane monooxygenase beta subunit

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

MacromoleculeName: Ammonia monooxygenase/methane monooxygenase, subunit C family protein
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: methane monooxygenase (soluble)
Source (natural)Organism: Methylococcus capsulatus str. Bath (bacteria) / Strain: Bath
Molecular weightTheoretical: 29.839309 KDa
SequenceString: MAATTIGGAA AAEAPLLDKK WLTFALAIYT VFYLWVRWYE GVYGWSAGLD SFAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRN LAALTPREEL RRNFTHLVWL VAYAWAIYWG ASYFTEQDGT WHQTIVRDTD FTPSHIIEFY LSYPIYIITG F AAFIYAKT ...String:
MAATTIGGAA AAEAPLLDKK WLTFALAIYT VFYLWVRWYE GVYGWSAGLD SFAPEFETYW MNFLYTEIVL EIVTASILWG YLWKTRDRN LAALTPREEL RRNFTHLVWL VAYAWAIYWG ASYFTEQDGT WHQTIVRDTD FTPSHIIEFY LSYPIYIITG F AAFIYAKT RLPFFAKGIS LPYLVLVVGP FMILPNVGLN EWGHTFWFME ELFVAPLHYG FVIFGWLALA VMGTLTQTFY SF AQGGLGQ SLCEAVDEGL IAK

UniProtKB: Ammonia monooxygenase/methane monooxygenase, subunit C family protein

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Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 9 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #5: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 5 / Number of copies: 18 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #6: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 6 / Number of copies: 18 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #7: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 7 / Number of copies: 12 / Formula: P1O
Molecular weightTheoretical: 566.728 Da
Chemical component information

ChemComp-P1O:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DDPC, phospholipid*YM

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Macromolecule #8: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #9: 1,2-dihexanoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1,2-dihexanoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 9 / Number of copies: 6 / Formula: HXG
Molecular weightTheoretical: 454.515 Da
Chemical component information

ChemComp-HXG:
1,2-dihexanoyl-sn-glycero-3-phosphocholine

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 401 / 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

Concentration5 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.57 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7s4h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 615783
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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