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- EMDB-39501: Cryo-EM structure of human lanosterol 14alpha-demethylase (CYP51)... -

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Basic information

Entry
Database: EMDB / ID: EMD-39501
TitleCryo-EM structure of human lanosterol 14alpha-demethylase (CYP51) in complex with FLZ
Map data
Sample
  • Complex: Lanosterol 14-alpha demethylase
    • Protein or peptide: Lanosterol 14-alpha demethylase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (~{E})-2-(2,5-dimethoxyphenyl)-~{N}-[2-(4-hydroxyphenyl)ethyl]-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide
KeywordsCYP51A1 / FLZ / cryo-EM / Parkinson's disease / Alzheimer's disease / PROTEIN BINDING
Function / homology
Function and homology information


cholesterol biosynthetic process via 24,25-dihydrolanosterol / sterol 14-demethylase activity / sterol 14alpha-demethylase / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / 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 / cholesterol biosynthetic process ...cholesterol biosynthetic process via 24,25-dihydrolanosterol / sterol 14-demethylase activity / sterol 14alpha-demethylase / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / 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 / 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
Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsZhou LC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human lanosterol 14alpha-demethylase (CYP51) in complex with FLZ
Authors: Zhou LC
History
DepositionMar 19, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39501.png

Downloads & links

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Map

FileDownload / File: emd_39501.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-2.4589643 - 3.2997663
Average (Standard dev.)0.0049709766 (±0.051239498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39501_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_39501_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 : Lanosterol 14-alpha demethylase

EntireName: Lanosterol 14-alpha demethylase
Components
  • Complex: Lanosterol 14-alpha demethylase
    • Protein or peptide: Lanosterol 14-alpha demethylase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (~{E})-2-(2,5-dimethoxyphenyl)-~{N}-[2-(4-hydroxyphenyl)ethyl]-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide

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Supramolecule #1: Lanosterol 14-alpha demethylase

SupramoleculeName: Lanosterol 14-alpha demethylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Lanosterol 14-alpha demethylase

MacromoleculeName: Lanosterol 14-alpha demethylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: sterol 14alpha-demethylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.470188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKKTSSKGK LPPYIFSPIP FLGHAIAFGK SPIEFLENAY EKYGPVFSFT MVGKTFTYLL GSDAAALLFN SKNEDLNAED VYSRLTTPV FGKGVAYDVP NPVFLEQKKM LKSGLNIAHF KQHVSIIEKE TKEYFESWGE SGEKNVFEAL SELIILTASH C LHGKEIRS ...String:
MAKKTSSKGK LPPYIFSPIP FLGHAIAFGK SPIEFLENAY EKYGPVFSFT MVGKTFTYLL GSDAAALLFN SKNEDLNAED VYSRLTTPV FGKGVAYDVP NPVFLEQKKM LKSGLNIAHF KQHVSIIEKE TKEYFESWGE SGEKNVFEAL SELIILTASH C LHGKEIRS QLNEKVAQLY ADLDGGFSHA AWLLPGWLPL PSFRRRDRAH REIKDIFYKA IQKRRQSQEK IDDILQTLLD AT YKDGRPL TDDEVAGMLI GLLLAGQHTS STTSAWMGFF LARDKTLQKK CYLEQKTVCG ENLPPLTYDQ LKDLNLLDRC IKE TLRLRP PIMIMMRMAR TPQTVAGYTI PPGHQVCVSP TVNQRLKDSW VERLDFNPDR YLQDNPASGE KFAYVPFGAG RHRC IGENF AYVQIKTIWS TMLRLYEFDL IDGYFPTVNY TTMIHTPENP VIRYKRRSKH HHH

UniProtKB: Lanosterol 14-alpha demethylase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: (~{E})-2-(2,5-dimethoxyphenyl)-~{N}-[2-(4-hydroxyphenyl)ethyl]-3-...

MacromoleculeName: (~{E})-2-(2,5-dimethoxyphenyl)-~{N}-[2-(4-hydroxyphenyl)ethyl]-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1D61
Molecular weightTheoretical: 449.496 Da

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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

BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287217
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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