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- PDB-6c6p: Human squalene epoxidase (SQLE, squalene monooxygenase) structure... -

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Basic information

Entry
Database: PDB / ID: 6c6p
TitleHuman squalene epoxidase (SQLE, squalene monooxygenase) structure with FAD and NB-598
ComponentsSqualene monooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Cholesterol Synthesis Pathway / SQLE / ERG1 / FAD-dependent Monooxygenase / Squalene hydroxylase / Squalene-2 / 3-epoxidase / FLAVOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


squalene monooxygenase / squalene monooxygenase activity / lipid droplet formation / sterol biosynthetic process / Cholesterol biosynthesis / cholesterol metabolic process / FAD binding / Activation of gene expression by SREBF (SREBP) / response to organic substance / regulation of cell population proliferation ...squalene monooxygenase / squalene monooxygenase activity / lipid droplet formation / sterol biosynthetic process / Cholesterol biosynthesis / cholesterol metabolic process / FAD binding / Activation of gene expression by SREBF (SREBP) / response to organic substance / regulation of cell population proliferation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Squalene epoxidase / Squalene monooxygenase / Squalene epoxidase / NAD(P)-binding Rossmann-like domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-EMV / FLAVIN-ADENINE DINUCLEOTIDE / Squalene monooxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsPadyana, A.K. / Jin, L.
Citation
Journal: Nat Commun / Year: 2019
Title: Structure and inhibition mechanism of the catalytic domain of human squalene epoxidase.
Authors: Padyana, A.K. / Gross, S. / Jin, L. / Cianchetta, G. / Narayanaswamy, R. / Wang, F. / Wang, R. / Fang, C. / Lv, X. / Biller, S.A. / Dang, L. / Mahoney, C.E. / Nagaraja, N. / Pirman, D. / ...Authors: Padyana, A.K. / Gross, S. / Jin, L. / Cianchetta, G. / Narayanaswamy, R. / Wang, F. / Wang, R. / Fang, C. / Lv, X. / Biller, S.A. / Dang, L. / Mahoney, C.E. / Nagaraja, N. / Pirman, D. / Sui, Z. / Popovici-Muller, J. / Smolen, G.A.
#1: Journal: To be published
Title: A chemical biology screen identifies a vulnerability of neuroendocrine cancer cells to SQLE inhibition.
Authors: Mahoney, C. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / Chen, Y. ...Authors: Mahoney, C. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / Chen, Y. / Gross, S. / Cianchetta, G. / Padyana, A.K. / Murray, S. / Liu, W. / Marks, K. / Murtie, J. / Dorsch, M. / Jin, S. / Nagaraja, N. / Biller, S.A. / Roddy, T. / Popovici-Muller, J. / Smolen, G.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Squalene monooxygenase
B: Squalene monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,56613
Polymers101,7922
Non-polymers6,77511
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-49 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.864, 127.864, 165.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-762-

HOH

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Components

#1: Protein Squalene monooxygenase / / Squalene epoxidase / SE


Mass: 50895.770 Da / Num. of mol.: 2 / Fragment: residues 118-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQLE, ERG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14534, squalene monooxygenase
#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Chemical ChemComp-EMV / (2E)-N-({3-[([3,3'-bithiophen]-5-yl)methoxy]phenyl}methyl)-N-ethyl-6,6-dimethylhept-2-en-4-yn-1-amine


Mass: 449.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31NOS2
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium sulfate, 0.1 M tri-Sodium citrate pH 5.6, 15 %(w/v) PEG 4000, 0.02 M Hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2016
RadiationMonochromator: Cryo-cooled double flat crystal Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→110.73 Å / Num. obs: 48368 / % possible obs: 88.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Χ2: 0.973 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.70.54123970.8020.2430.5980.87188
2.54-2.594.80.46423940.8570.2060.5110.90590.3
2.59-2.644.80.42824500.8960.1890.4710.89990
2.64-2.694.80.34624480.9220.1540.3820.93590.5
2.69-2.754.90.28324460.9420.1250.3120.98290.1
2.75-2.824.80.24224380.9630.1060.2661.00890.1
2.82-2.894.80.22324150.9610.0980.2461.03690.1
2.89-2.964.80.1824230.9750.080.1991.03390
2.96-3.054.80.15624430.980.0680.1721.03389.7
3.05-3.154.80.13824130.9820.0610.1521.08490.2
3.15-3.264.80.1224810.9860.0530.1330.93489.5
3.26-3.394.80.10124150.9890.0460.1120.94489.5
3.39-3.554.80.09124580.9910.0410.1010.93689.2
3.55-3.734.70.08224210.9920.0370.0910.96489.2
3.73-3.974.70.07723940.9920.0350.0850.93988.2
3.97-4.274.60.07624150.9910.0350.0840.98987.1
4.27-4.74.50.07323970.990.0340.0811.00987.8
4.7-5.384.50.07223970.9920.0330.081.04985.9
5.38-6.784.60.06723590.9940.0310.0740.99184.5
6.78-504.70.05523640.9940.0260.0620.91980.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
REFMACphasing
RefinementResolution: 2.5→40.57 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.4
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 2315 4.79 %RANDOM
Rwork0.1931 ---
obs0.195 48318 88.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 363 170 7569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027616
X-RAY DIFFRACTIONf_angle_d0.51310389
X-RAY DIFFRACTIONf_dihedral_angle_d16.8374559
X-RAY DIFFRACTIONf_chiral_restr0.0411186
X-RAY DIFFRACTIONf_plane_restr0.0041266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4983-2.54920.34051130.27292699X-RAY DIFFRACTION89
2.5492-2.60470.27681280.24592730X-RAY DIFFRACTION90
2.6047-2.66520.29541480.22942713X-RAY DIFFRACTION90
2.6652-2.73190.29121610.22762698X-RAY DIFFRACTION90
2.7319-2.80570.28771300.22912721X-RAY DIFFRACTION90
2.8057-2.88830.30131290.23662738X-RAY DIFFRACTION90
2.8883-2.98150.28771540.23922734X-RAY DIFFRACTION90
2.9815-3.0880.28031320.22382717X-RAY DIFFRACTION90
3.088-3.21160.25421390.23542756X-RAY DIFFRACTION90
3.2116-3.35770.25511470.22832687X-RAY DIFFRACTION89
3.3577-3.53460.27681670.21812700X-RAY DIFFRACTION90
3.5346-3.75590.28071330.19922712X-RAY DIFFRACTION89
3.7559-4.04570.2161140.17662722X-RAY DIFFRACTION88
4.0457-4.45230.20011380.16632702X-RAY DIFFRACTION88
4.4523-5.09550.19241390.15862664X-RAY DIFFRACTION86
5.0955-6.41570.21121220.17942669X-RAY DIFFRACTION85
6.4157-40.57520.16851210.1592641X-RAY DIFFRACTION81

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