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- PDB-3n9y: Crystal structure of human CYP11A1 in complex with cholesterol -

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Basic information

Entry
Database: PDB / ID: 3n9y
TitleCrystal structure of human CYP11A1 in complex with cholesterol
Components
  • AdrenodoxinAdrenal ferredoxin
  • Cholesterol side-chain cleavage enzyme
KeywordsOxidoreductase / Electron transport / cytochrome P450 / cholesterol side chain cleavage / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cholesterol monooxygenase (side-chain-cleaving) / cholesterol monooxygenase (side-chain-cleaving) activity / Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / cortisol metabolic process / Mitochondrial iron-sulfur cluster biogenesis / glucocorticoid biosynthetic process / hormone biosynthetic process / P450-containing electron transport chain / sterol metabolic process ...cholesterol monooxygenase (side-chain-cleaving) / cholesterol monooxygenase (side-chain-cleaving) activity / Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / cortisol metabolic process / Mitochondrial iron-sulfur cluster biogenesis / glucocorticoid biosynthetic process / hormone biosynthetic process / P450-containing electron transport chain / sterol metabolic process / vitamin D metabolic process / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / steroid biosynthetic process / cellular response to peptide hormone stimulus / electron transport chain / Endogenous sterols / cellular response to forskolin / cellular response to cAMP / cholesterol metabolic process / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Cytochrome P450, E-class, group I / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Cytochrome P450, E-class, group I / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CHOLESTEROL / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Cholesterol side-chain cleavage enzyme, mitochondrial / Adrenodoxin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStrushkevich, N.V. / MacKenzie, F. / Tempel, W. / Botchkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J.U. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system.
Authors: Strushkevich, N. / Mackenzie, F. / Cherkesova, T. / Grabovec, I. / Usanov, S. / Park, H.W.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Cholesterol side-chain cleavage enzyme
B: Cholesterol side-chain cleavage enzyme
C: Adrenodoxin
D: Adrenodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27010
Polymers138,9124
Non-polymers2,3586
Water9,098505
1
A: Cholesterol side-chain cleavage enzyme
C: Adrenodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6355
Polymers69,4562
Non-polymers1,1793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-44 kcal/mol
Surface area23030 Å2
MethodPISA
2
B: Cholesterol side-chain cleavage enzyme
D: Adrenodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6355
Polymers69,4562
Non-polymers1,1793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-43 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.999, 114.686, 86.019
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Cholesterol side-chain cleavage enzyme / / Cytochrome P450 11A1 / CYPXIA1 / Cytochrome P450(scc) / Cholesterol desmolase


Mass: 56885.066 Da / Num. of mol.: 2 / Fragment: UNP residues 41-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP11A, CYP11A1 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P05108, cholesterol monooxygenase (side-chain-cleaving)
#2: Protein Adrenodoxin / Adrenal ferredoxin / Adrenal ferredoxin / Ferredoxin-1 / Hepatoredoxin


Mass: 12571.036 Da / Num. of mol.: 2 / Fragment: UNP residues 62-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: adrenodoxin, ADX, FDX1 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P10109

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Non-polymers , 4 types, 511 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.88 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, Ca acetate, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDate: Mar 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 92214 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.084 / Χ2: 1.576 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.144.40.52246370.9541100
2.14-2.174.40.44445840.9711100
2.17-2.224.40.39746080.961100
2.22-2.264.40.35945821.187199.9
2.26-2.314.40.30546011.0681100
2.31-2.364.40.25845671.0471100
2.36-2.424.40.2345891.0981100
2.42-2.494.50.19346221.1291100
2.49-2.564.40.17545671.1731100
2.56-2.644.40.15645901.2231100
2.64-2.744.40.13546341.321100
2.74-2.854.40.11245941.4061100
2.85-2.984.40.09746321.5181100
2.98-3.134.40.08745871.7031100
3.13-3.334.40.07546511.9931100
3.33-3.594.40.06945862.4811100
3.59-3.944.30.06446413.056199.9
3.94-4.514.20.05246092.946199.9
4.51-5.664.10.04246522.403199.8
5.66-204.30.03646812.109199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.89 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.368 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4576 5 %RANDOM
Rwork0.205 ---
obs0.207 91667 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.11 Å2 / Biso mean: 34.661 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0.74 Å2
2---2.09 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 150 505 9447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229192
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.98712507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34651073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85623.6450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.931151535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2631564
X-RAY DIFFRACTIONr_chiral_restr0.090.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217008
X-RAY DIFFRACTIONr_mcbond_it0.6661.55375
X-RAY DIFFRACTIONr_mcangle_it1.28628709
X-RAY DIFFRACTIONr_scbond_it1.8333817
X-RAY DIFFRACTIONr_scangle_it3.0664.53794
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 342 -
Rwork0.246 6372 -
all-6714 -
obs--100 %

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