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- PDB-9ef0: EM structure of cytochrome P450 reductase -

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Basic information

Entry
Database: PDB / ID: 9ef0
TitleEM structure of cytochrome P450 reductase
ComponentsNADPH--cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome P450 reductase / CPR / POR / electron transfer / endoplasmic reticulum / flavoprotein
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / nitrate catabolic process / organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / cytochrome-b5 reductase activity, acting on NAD(P)H ...iron-cytochrome-c reductase activity / positive regulation of growth plate cartilage chondrocyte proliferation / nitrate catabolic process / organofluorine metabolic process / demethylation / carnitine metabolic process / flavonoid metabolic process / nitric oxide dioxygenase NAD(P)H activity / cellular response to gonadotropin stimulus / cytochrome-b5 reductase activity, acting on NAD(P)H / nitric oxide catabolic process / positive regulation of steroid hormone biosynthetic process / positive regulation of chondrocyte differentiation / cellular response to follicle-stimulating hormone stimulus / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / cellular response to peptide hormone stimulus / response to dexamethasone / fatty acid oxidation / response to hormone / nitric oxide biosynthetic process / response to nutrient / electron transport chain / FMN binding / flavin adenine dinucleotide binding / NADP binding / electron transfer activity / oxidoreductase activity / hydrolase activity / response to xenobiotic stimulus / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cytosol
Similarity search - Function
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 ...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 / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / NADPH--cytochrome P450 reductase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsLepesheva, G.I. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151876 United States
CitationJournal: To be Published
Title: Structural state of cytochrome P450 reductase in solution
Authors: Lepesheva, G.I. / Ren, Y.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH--cytochrome P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3003
Polymers77,0581
Non-polymers1,2422
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein NADPH--cytochrome P450 reductase / CPR / P450R


Mass: 77057.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Por / Production host: Escherichia coli (E. coli) / References: UniProt: P00388, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Has ligand of interestN
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: Cytochrome P450 reductase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.078 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: PBS
SpecimenConc.: 0.23 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: OTHER
Electron lensMode: OTHER / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 90 K / Temperature (max): 90 K / Temperature (min): 90 K
Image recordingAverage exposure time: 0.899 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31000

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2EPU2.1.4image acquisition
7UCSF Chimera1.16model fitting
9PHENIX1.21.1_5286:model refinement
12cryoSPARC4.6classification
CTF correctionType: NONE
Particle selectionNum. of particles selected: 30000000
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 671545 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025171
ELECTRON MICROSCOPYf_angle_d0.5227026
ELECTRON MICROSCOPYf_dihedral_angle_d9.243802
ELECTRON MICROSCOPYf_chiral_restr0.04738
ELECTRON MICROSCOPYf_plane_restr0.004901

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