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- PDB-3wkt: Complex structure of an open form of NADPH-cytochrome P450 reduct... -

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Basic information

Entry
Database: PDB / ID: 3wkt
TitleComplex structure of an open form of NADPH-cytochrome P450 reductase and heme oxygenase-1
Components
  • Heme oxygenase 1
  • NADPH-cytochrome P450 reductase
KeywordsOXIDOREDUCTASE / Heme degradation / Microsomal membrane
Function / homology
Function and homology information


iron-cytochrome-c reductase activity / arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / organofluorine metabolic process / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / carnitine metabolic process ...iron-cytochrome-c reductase activity / arachidonate omega-hydroxylase activity / Regulation of HMOX1 expression and activity / nitrate catabolic process / organofluorine metabolic process / Iron uptake and transport / demethylation / response to 3-methylcholanthrene / Heme degradation / carnitine metabolic process / flavonoid metabolic process / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / nitric oxide dioxygenase NAD(P)H activity / heme metabolic process / cellular response to gonadotropin stimulus / regulation of growth plate cartilage chondrocyte proliferation / 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 / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / negative regulation of muscle cell apoptotic process / wound healing involved in inflammatory response / cellular response to cisplatin / cellular response to follicle-stimulating hormone stimulus / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / heme catabolic process / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / positive regulation of smoothened signaling pathway / negative regulation of mast cell cytokine production / positive regulation of epithelial cell apoptotic process / phospholipase D activity / cellular response to peptide hormone stimulus / epithelial cell apoptotic process / negative regulation of ferroptosis / erythrocyte homeostasis / regulation of cholesterol metabolic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / cellular response to cadmium ion / response to dexamethasone / negative regulation of vascular associated smooth muscle cell proliferation / fatty acid oxidation / positive regulation of macroautophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phospholipid metabolic process / response to hormone / nitric oxide biosynthetic process / response to nutrient / liver regeneration / response to nicotine / positive regulation of smooth muscle cell proliferation / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of cholesterol biosynthetic process / electron transport chain / caveola / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / FMN binding / NADP binding / flavin adenine dinucleotide binding / cellular response to heat / angiogenesis / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / response to oxidative stress / electron transfer activity / oxidoreductase activity / response to hypoxia / hydrolase activity / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus
Similarity search - Function
NADPH-cytochrome P450 reductase / Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Haem oxygenase-like, multi-helical / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain ...NADPH-cytochrome P450 reductase / Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Haem oxygenase-like, multi-helical / 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 / PROTOPORPHYRIN IX CONTAINING FE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH--cytochrome P450 reductase / Heme oxygenase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsSugishima, M. / Sato, H. / Higashimoto, Y. / Harada, J. / Wada, K. / Fukuyama, K. / Noguchi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the electron transfer from an open form of NADPH-cytochrome P450 oxidoreductase to heme oxygenase.
Authors: Sugishima, M. / Sato, H. / Higashimoto, Y. / Harada, J. / Wada, K. / Fukuyama, K. / Noguchi, M.
History
DepositionOct 31, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-cytochrome P450 reductase
B: NADPH-cytochrome P450 reductase
C: Heme oxygenase 1
D: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,99312
Polymers201,7894
Non-polymers5,2048
Water00
1
A: NADPH-cytochrome P450 reductase
C: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4966
Polymers100,8952
Non-polymers2,6024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-cytochrome P450 reductase
D: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4966
Polymers100,8952
Non-polymers2,6024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)290.336, 290.336, 83.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSERAA70 - 67414 - 618
21VALVALSERSERBB70 - 67414 - 618
12SERSERGLUGLUCC10 - 22310 - 223
22SERSERGLUGLUDD10 - 22310 - 223

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 70282.102 Da / Num. of mol.: 2 / Mutation: UNP RESIDUES 58-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Por / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00388, NADPH-hemoprotein reductase
#2: Protein Heme oxygenase 1 / HO-1 / HSP32


Mass: 30612.496 Da / Num. of mol.: 2 / Mutation: UNP RESIDUES 1-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06762, heme oxygenase (biliverdin-producing)

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.04 Å3/Da / Density % sol: 75.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 18% PEG 6000, 0.2M sodium acetate, 0.1M Tris-HCl, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 8, 2013
RadiationMonochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. all: 26421 / Num. obs: 26421 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rsym value: 0.107 / Net I/σ(I): 6.2
Reflection shellResolution: 4.3→4.37 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.651 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ES9, 1DVE

3es9

1dve


Resolution: 4.3→41.34 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.926 / SU B: 40.743 / SU ML: 0.521 / Cross valid method: THROUGHOUT / ESU R Free: 0.796 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25599 1400 5 %RANDOM
Rwork0.22226 ---
obs0.224 26421 99.82 %-
all-28221 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 234.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.35 Å20 Å2
2---0.35 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 4.3→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13038 0 316 0 13354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.98318615
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89551611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.67623.917674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.795152289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.811590
X-RAY DIFFRACTIONr_chiral_restr0.1240.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110507
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6050.18
12B6050.18
21C1550.21
22D1550.21
LS refinement shellResolution: 4.299→4.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 97 -
Rwork0.362 1962 -
obs--100 %

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