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- PDB-3sn5: Crystal structure of human CYP7A1 in complex with cholest-4-en-3-one -

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Basic information

Entry
Database: PDB / ID: 3sn5
TitleCrystal structure of human CYP7A1 in complex with cholest-4-en-3-one
ComponentsCholesterol 7-alpha-monooxygenase
KeywordsOXIDOREDUCTASE / cytochrome P450 / cholesterol 7-alpha hydroxylase / CYP7A1 / cholest-4-en-3-one / bile acid biosynthesis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cholesterol 7alpha-monooxygenase / 24-hydroxycholesterol 7alpha-hydroxylase / cholesterol 7-alpha-monooxygenase activity / 24-hydroxycholesterol 7alpha-hydroxylase activity / negative regulation of collagen biosynthetic process / cellular response to cholesterol / sterol metabolic process / negative regulation of fatty acid biosynthetic process / regulation of bile acid biosynthetic process / positive regulation of cholesterol biosynthetic process ...cholesterol 7alpha-monooxygenase / 24-hydroxycholesterol 7alpha-hydroxylase / cholesterol 7-alpha-monooxygenase activity / 24-hydroxycholesterol 7alpha-hydroxylase activity / negative regulation of collagen biosynthetic process / cellular response to cholesterol / sterol metabolic process / negative regulation of fatty acid biosynthetic process / regulation of bile acid biosynthetic process / positive regulation of cholesterol biosynthetic process / bile acid biosynthetic process / bile acid and bile salt transport / bile acid signaling pathway / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cholesterol catabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cholesterol homeostasis / cellular response to glucose stimulus / PPARA activates gene expression / response to ethanol / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cholesterol 7-alpha-monooxygenase / Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cholesterol 7-alpha-monooxygenase / Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE / Cytochrome P450 7A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsStrushkevich, N. / Tempel, W. / MacKenzie, F. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human CYP7A1 in complex with cholest-4-en-3-one
Authors: Strushkevich, N. / Tempel, W. / MacKenzie, F. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_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

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Assembly

Deposited unit
A: Cholesterol 7-alpha-monooxygenase
B: Cholesterol 7-alpha-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,96614
Polymers112,9642
Non-polymers2,00212
Water64936
1
A: Cholesterol 7-alpha-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4837
Polymers56,4821
Non-polymers1,0016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cholesterol 7-alpha-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4837
Polymers56,4821
Non-polymers1,0016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.160, 137.630, 160.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cholesterol 7-alpha-monooxygenase / CYP7A1 / CYPVII / Cholesterol 7-alpha-hydroxylase / Cytochrome P450 7A1


Mass: 56481.836 Da / Num. of mol.: 2 / Fragment: UNP residues 25-503 / Mutation: T104L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP7A1, CYP7 / Plasmid: pCW-LIC-29 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P22680, EC: 1.14.13.17
#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-K2B / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE


Mass: 384.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44O
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.9 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 18% PEG550 MME, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 33172 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.448 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.75-2.820.992.4181742435100
2.82-2.90.7862.9174382323100
2.9-2.980.5883.8171862297100
2.98-3.070.474.7166822224100
3.07-3.180.3725.8160852145100
3.18-3.290.2887.215792211599.9
3.29-3.410.2219.1150712008100
3.41-3.550.16111.8146001962100
3.55-3.710.12614.213931187399.9
3.71-3.890.09917.2131231764100
3.89-4.10.08719.612790172599.8
4.1-4.350.07123.2121571648100
4.35-4.650.06425.6111971524100
4.65-5.020.0626.5104591429100
5.02-5.50.0626.797081333100
5.5-6.150.06426.687171210100
6.15-7.10.05827.577101083100
7.1-8.70.05231.46380915100
8.7-12.30.04734.2496974299.9
12.30.04732.3251641790.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DAX

3dax


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9177 / Occupancy max: 1 / Occupancy min: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
Details: Cholestenone restraints are based on PDB entry 2X5W and were optimized on the prodrg server. Solvent atoms were added based on peaks in the Fo-Fc map. Non-crystallographic symmetry in the ...Details: Cholestenone restraints are based on PDB entry 2X5W and were optimized on the prodrg server. Solvent atoms were added based on peaks in the Fo-Fc map. Non-crystallographic symmetry in the peak positions was considered in the rejection and addition of some sites. Solvent atoms were not included in refinement and structure factor calculation. Some of the assigned water positions likely represent other molecule/atom/ion types. REFMAC, Phenix, coot, and the molprobity server were also used.
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 1775 5.36 %THIN SHELLS (SFTOOLS)
Rwork0.1824 ---
obs0.1845 33114 --
Displacement parametersBiso max: 213.76 Å2 / Biso mean: 77.1253 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-7.2742 Å20 Å20 Å2
2--2.9195 Å20 Å2
3----10.1937 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 150 36 7401
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2448SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes157HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1129HARMONIC5
X-RAY DIFFRACTIONt_it7492HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion986SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8381SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7554HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg10301HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion17.74
LS refinement shellResolution: 2.75→2.83 Å / Total num. of bins used: 17 /
RfactorNum. reflection
Rwork0.2229 2836
all0.2229 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6948-0.1511-0.17132.51231.51163.19840.07740.0631-0.20590.26050.1644-0.24690.22990.2599-0.2418-0.24360.0189-0.0785-0.166-0.1131-0.004519.8594-1.0888-22.1778
21.206-0.86810.16664.1852-0.83112.64960.16690.05590.1332-0.2518-0.09490.39080.021-0.043-0.072-0.24660.032-0.0649-0.2046-0.0168-0.0948-4.522135.1609-27.0853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A24 - 1429
2X-RAY DIFFRACTION2{ B|* }B25 - 1429

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