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- EMDB-27536: CYP102A1 in Closed Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-27536
TitleCYP102A1 in Closed Conformation
Map data
Sample
  • Complex: CYP102A1
    • Protein or peptide: Bifunctional cytochrome P450/NADPH--P450 reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: SULFATE ION
  • Ligand: TETRAETHYLENE GLYCOL
Keywordscytochrome P450 electron transfer protein dynamic CYP102A1 / OXIDOREDUCTASE
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSu M / Xu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM
Authors: Su M / Xu H
History
DepositionJul 8, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27536.png

Downloads & links

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Map

FileDownload / File: emd_27536.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 180 pix.
= 363.6 Å		2.02 Å/pix.
x 180 pix.
= 363.6 Å		2.02 Å/pix.
x 180 pix.
= 363.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.143026 - 5.4600677
Average (Standard dev.)0.0012281248 (±0.12800443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 363.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27536_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_27536_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 : CYP102A1

EntireName: CYP102A1
Components
  • Complex: CYP102A1
    • Protein or peptide: Bifunctional cytochrome P450/NADPH--P450 reductase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: SULFATE ION
  • Ligand: TETRAETHYLENE GLYCOL

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Supramolecule #1: CYP102A1

SupramoleculeName: CYP102A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: BM3 CYP102A
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Bifunctional cytochrome P450/NADPH--P450 reductase

MacromoleculeName: Bifunctional cytochrome P450/NADPH--P450 reductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19
Molecular weightTheoretical: 116.887188 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTIKEMPQPK TFGELKNLPL LNTDKPVQAL MKIADELGEI FKFEAPGRVT RYLSSQRLIK EACDESRFDK NLSQALKFVR DFFGDGLFT SWTHEKNWKK AHNILLPSFS QQAMKGYHAM MVDIAVQLVQ KWERLNADEH IEVPEDMTRL TLDTIGLCGF N YRFNSFYR ...String:
MTIKEMPQPK TFGELKNLPL LNTDKPVQAL MKIADELGEI FKFEAPGRVT RYLSSQRLIK EACDESRFDK NLSQALKFVR DFFGDGLFT SWTHEKNWKK AHNILLPSFS QQAMKGYHAM MVDIAVQLVQ KWERLNADEH IEVPEDMTRL TLDTIGLCGF N YRFNSFYR DQPHPFITSM VRALDEAMNK LQRANPDDPA YDENKRQFQE DIKVMNDLVD KIIADRKASG EQSDDLLTHM LN GKDPETG EPLDDENIRY QIITFLIAGH ETTSGLLSFA LYFLVKNPHV LQKAAEEAAR VLVDPVPSYK QVKQLKYVGM VLN EALRLW PTAPAFSLYA KEDTVLGGEY PLEKGDELMV LIPQLHRDKT IWGDDVEEFR PERFENPSAI PQHAFKPFGN GQRA CIGQQ FALHEATLVL GMMLKHFDFE DHTNYELDIK ETLTLKPEGF VVKAKSKKIP LKKVRKKAEN AHNTPLLVLY GSNMG TAEG TARDLADIAM SKGFAPQVAT LDSHAGNLPR EGAVLIVTAS YNGHPPDNAK QFVDWLDQAS ADEVKGVRYS VFGCGD KNW ATTYQKVPAF IDETLAAKGA ENIADRGEAD ASDDFEGTYE EWREHMWSDV AAYFNLDIEN SEDNKSTLSL QFVDSAA DM PLAKMHGAFS TNVVASKELQ QPGSARSTRH LEIELPKEAS YQEGDHLGVI PRNYEGIVNR VTARFGLDAS QQIRLEAE E EKLAHLPLAK TVSVEELLQY VELQDPVTRT QLRAMAAKTV CPPHKVELEA LLEKQAYKEQ VLAKRLTMLE LLEKYPACE MKFSEFIALL PSIRPRYYSI SSSPRVDEKQ ASITVSVVSG EAWSGYGEYK GIASNYLAEL QEGDTITCFI STPQSEFTLP KDPETPLIM VGPGTGVAPF RGFVQARKQL KEQGQSLGEA HLYFGCRSPH EDYLYQEELE NAQSEGIITL HTAFSRMPNQ P KTYVQHVM EQDGKKLIEL LDQGAHFYIC GDGSQMAPAV EATLMKSYAD VHQVSEADAR LWLQQLEEKG RYAKDVWAG

UniProtKB: Bifunctional cytochrome P450/NADPH--P450 reductase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl...

MacromoleculeName: 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole
type: ligand / ID: 3 / Number of copies: 2 / Formula: 1C6
Molecular weightTheoretical: 329.417 Da
Chemical component information

ChemComp-1C6:
6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole / medication*YM

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Macromolecule #4: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #6: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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Macromolecule #7: TETRAETHYLENE GLYCOL

MacromoleculeName: TETRAETHYLENE GLYCOL / type: ligand / ID: 7 / Number of copies: 4 / Formula: PG4
Molecular weightTheoretical: 194.226 Da
Chemical component information

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

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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: 7.4 / Component - Concentration: 50.0 mM / Component - Formula: K2HPO4-KH2PO4-KCL / Component - Name: sodium phosphate + potassium chloride
Details: Fresh prepare sodium phosphate (50mM) + potassium chloride (150mM), pH7.4 and filter with 0.22um filters.
GridModel: UltrAuFoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe CYP102A1 sample purify and concentrated to 5mg/ml.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249374
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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