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- PDB-6c6n: Human squalene epoxidase (SQLE, squalene monooxygenase) structure... -

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Basic information

Entry
Database: PDB / ID: 6c6n
TitleHuman squalene epoxidase (SQLE, squalene monooxygenase) structure with FAD and Cmpd-4"
ComponentsSqualene monooxygenase
KeywordsFLAVOPROTEIN/INHIBITOR / Cholesterol Synthesis Pathway / SQLE / ERG1 / FAD-dependent Monooxygenase / Squalene hydroxylase / Squalene-2 / 3-epoxidase / FLAVOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / FLAVOPROTEIN-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-EKV / FLAVIN-ADENINE DINUCLEOTIDE / Squalene monooxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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: Nat Commun / Year: 2019
Title: A chemical biology screen identifies a vulnerability of neuroendocrine cancer cells to SQLE inhibition.
Authors: Mahoney, C.E. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E.L. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / ...Authors: Mahoney, C.E. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E.L. / 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.M. / Murtie, J. / Dorsch, M. / Jin, S. / Nagaraja, N. / Biller, S.A. / Roddy, T. / Popovici-Muller, J. / Smolen, G.A.
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.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _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)109,12319
Polymers101,7922
Non-polymers7,33117
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-82 kcal/mol
Surface area34780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.960, 126.960, 166.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 196 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-EKV / N-[(3-{[dimethyl(2-methylphenyl)silyl]methoxy}phenyl)methyl]-N-ethyl-6-methoxy-6-methylhepta-2,4-diyn-1-amine


Mass: 447.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H37NO2Si
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.86 Å3/Da / Density % sol: 68.13 %
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, 15-18 %(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: 0.97941 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2016
RadiationMonochromator: Cryo-cooled double flat crystal Si (III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.3→109.951 Å / Num. all: 68439 / Num. obs: 68439 / % possible obs: 99 % / Redundancy: 5.2 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.09 / Rsym value: 0.082 / Net I/av σ(I): 6.7 / Net I/σ(I): 12.1 / Num. measured all: 355239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.3-2.425.30.5551.499250.2490.6140.55599.6
2.42-2.575.30.3921.994360.1750.4330.39299.6
2.57-2.755.30.2552.988420.1130.2820.25599
2.75-2.975.30.1624.581940.0720.1790.16298.8
2.97-3.255.10.1096.476550.0480.120.10999.6
3.25-3.6450.0699.168900.0320.0770.06999.2
3.64-4.24.90.05810.561720.0270.0650.058100
4.2-5.145.40.05211.452380.0240.0580.05299.9
5.14-7.275.30.05310.840980.0230.0580.05399.6
7.27-37.1654.80.04812.619890.0230.0540.04884.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
AutoSolphasing
RefinementResolution: 2.3→37.165 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3349 4.9 %RANDOM
Rwork0.189 ---
obs0.1905 68379 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 401 179 7632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037653
X-RAY DIFFRACTIONf_angle_d0.57110433
X-RAY DIFFRACTIONf_dihedral_angle_d15.3984575
X-RAY DIFFRACTIONf_chiral_restr0.0421186
X-RAY DIFFRACTIONf_plane_restr0.0041264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33290.29371410.24152672X-RAY DIFFRACTION100
2.3329-2.36770.25871420.22352693X-RAY DIFFRACTION100
2.3677-2.40470.25911690.21022687X-RAY DIFFRACTION99
2.4047-2.44410.27471270.22022737X-RAY DIFFRACTION99
2.4441-2.48620.25481550.222669X-RAY DIFFRACTION100
2.4862-2.53140.29281310.21992703X-RAY DIFFRACTION99
2.5314-2.58010.27511370.21012692X-RAY DIFFRACTION99
2.5801-2.63270.22591340.21062686X-RAY DIFFRACTION99
2.6327-2.690.28731510.21362685X-RAY DIFFRACTION99
2.69-2.75250.26171210.21812716X-RAY DIFFRACTION99
2.7525-2.82130.26131220.22262729X-RAY DIFFRACTION99
2.8213-2.89760.29461110.2252665X-RAY DIFFRACTION98
2.8976-2.98280.29261350.22482693X-RAY DIFFRACTION99
2.9828-3.07910.25331110.22952749X-RAY DIFFRACTION100
3.0791-3.1890.25621360.23532710X-RAY DIFFRACTION99
3.189-3.31670.26641560.22672750X-RAY DIFFRACTION100
3.3167-3.46750.25181600.21532646X-RAY DIFFRACTION99
3.4675-3.65020.23311360.18882736X-RAY DIFFRACTION99
3.6502-3.87860.21541410.18362762X-RAY DIFFRACTION100
3.8786-4.17770.17331710.16132732X-RAY DIFFRACTION100
4.1777-4.59750.16471240.15282788X-RAY DIFFRACTION100
4.5975-5.26110.17641680.14432757X-RAY DIFFRACTION100
5.2611-6.62240.1841360.17092794X-RAY DIFFRACTION99
6.6224-37.170.19021340.16172579X-RAY DIFFRACTION88

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