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- PDB-6uez: Human sterol 14a-demethylase (CYP51) in complex with the substrat... -

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Basic information

Entry
Database: PDB / ID: 6uez
TitleHuman sterol 14a-demethylase (CYP51) in complex with the substrate lanosterol
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / monooxygenase / sterol biosynthesis / cytochrome P450 / substrate-induced conformational change
Function / homology
Function and homology information


sterol 14alpha-demethylase / sterol 14-demethylase activity / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / Endogenous sterols ...sterol 14alpha-demethylase / sterol 14-demethylase activity / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / Endogenous sterols / Activation of gene expression by SREBF (SREBP) / negative regulation of protein catabolic process / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / membrane
Similarity search - Function
: / Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / LANOSTEROL / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Lepesheva, G.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01067871 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A requirement for an active proton delivery network supports a compound I-mediated C-C bond cleavage in CYP51 catalysis.
Authors: Hargrove, T.Y. / Wawrzak, Z. / Guengerich, F.P. / Lepesheva, G.I.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6996
Polymers103,6132
Non-polymers2,0864
Water9,260514
1
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8503
Polymers51,8071
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8503
Polymers51,8071
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.180, 165.070, 154.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Lanosterol 14-alpha demethylase / LDM / CYPLI / Cytochrome P450 51A1 / Cytochrome P450-14DM / Cytochrome P45014DM / Cytochrome P450LI ...LDM / CYPLI / Cytochrome P450 51A1 / Cytochrome P450-14DM / Cytochrome P45014DM / Cytochrome P450LI / Sterol 14-alpha demethylase


Mass: 51806.531 Da / Num. of mol.: 2 / Fragment: UNP residues 61-503 / Mutation: D231A, H314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP51A1, CYP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16850, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-LAN / LANOSTEROL


Mass: 426.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H50O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4 / Details: PEG3350, HEGA-11, potassium phosphate, lanosterol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.98→43.6 Å / Num. obs: 68672 / % possible obs: 89.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.056 / Net I/av σ(I): 16.1 / Net I/σ(I): 16.1
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2937 / % possible all: 52.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4UHI

4uhi


Resolution: 1.98→43.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.004 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.157
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 3792 5.2 %RANDOM
Rwork0.191 ---
obs0.1927 68672 89.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 235.78 Å2 / Biso mean: 53.135 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å2-0 Å2
2---0.44 Å20 Å2
3----1.75 Å2
Refinement stepCycle: final / Resolution: 1.98→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7127 0 148 515 7790
Biso mean--39.36 57.89 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137521
X-RAY DIFFRACTIONr_bond_other_d0.0090.0177035
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.67110235
X-RAY DIFFRACTIONr_angle_other_deg1.3871.58416313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47521.59390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.922151280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0781550
X-RAY DIFFRACTIONr_chiral_restr0.0710.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028295
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021639
X-RAY DIFFRACTIONr_rigid_bond_restr6.227314553
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 179 -
Rwork0.342 2937 -
all-3116 -
obs--52.78 %

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