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- PDB-3na0: Crystal structure of human CYP11A1 in complex with 20,22-dihydrox... -

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Basic information

Entry
Database: PDB / ID: 3na0
TitleCrystal structure of human CYP11A1 in complex with 20,22-dihydroxycholesterol
Components
  • Adrenodoxin, mitochondrialAdrenal ferredoxin
  • Cholesterol side-chain cleavage enzyme, mitochondrial
KeywordsOxidoreductase / Electron transport / cytochrome P450 / 20 / 22-dihydroxycholesterol / 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 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 ...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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3alpha,8alpha,22R)-cholest-5-ene-3,20,22-triol / 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: 2.5 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 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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_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, mitochondrial
B: Cholesterol side-chain cleavage enzyme, mitochondrial
C: Adrenodoxin, mitochondrial
D: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,27710
Polymers124,8554
Non-polymers2,4226
Water5,242291
1
A: Cholesterol side-chain cleavage enzyme, mitochondrial
C: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6385
Polymers62,4272
Non-polymers1,2113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cholesterol side-chain cleavage enzyme, mitochondrial
D: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6385
Polymers62,4272
Non-polymers1,2113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.806, 114.724, 85.716
Angle α, β, γ (deg.)90.000, 101.780, 90.000
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, mitochondrial / / Cytochrome P450 11A1 / CYPXIA1 / Cytochrome P450(scc) / Cholesterol desmolase


Mass: 54911.035 Da / Num. of mol.: 2 / Fragment: UNP residues 44-514
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, mitochondrial / Adrenal ferredoxin / Adrenal ferredoxin / Ferredoxin-1 / Hepatoredoxin


Mass: 7516.367 Da / Num. of mol.: 2 / Fragment: UNP residues 88-155
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, 297 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-2DC / (3alpha,8alpha,22R)-cholest-5-ene-3,20,22-triol / 20α,22R-Dihydroxycholesterol


Mass: 418.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O3 / Comment: hormone*YM
#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.: 291 / 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: 3.19 Å3/Da / Density % sol: 61.47 %
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: 23-ID-B
DetectorDate: Nov 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 53587 / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.105 / Χ2: 0.926 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.543.60.36524390.787189.8
2.54-2.593.70.35625090.849191.7
2.59-2.643.80.33825340.836194.8
2.64-2.693.90.32326370.948196.9
2.69-2.754.10.30626540.821197.4
2.75-2.824.20.26426420.804199.1
2.82-2.894.30.2427240.84199.4
2.89-2.964.40.22627120.83199.8
2.96-3.054.50.20627120.8321100
3.05-3.154.60.1827000.8591100
3.15-3.264.70.15227200.8511100
3.26-3.394.70.12827000.8641100
3.39-3.554.70.10827390.904199.9
3.55-3.734.70.08827230.958199.9
3.73-3.974.70.07927191.0281100
3.97-4.274.70.06827221.111199.9
4.27-4.74.70.05727131.081100
4.7-5.384.70.05327370.9691100
5.38-6.784.70.06227540.9891100
6.78-504.60.04327971.1871100

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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: 2.5→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.702 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2718 5.1 %RANDOM
Rwork0.201 ---
obs0.203 53564 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.26 Å2 / Biso mean: 29.281 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-1.13 Å2
2---1.68 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8138 0 154 291 8583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228528
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.98911602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10423.478414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.232151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6731560
X-RAY DIFFRACTIONr_chiral_restr0.0870.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216486
X-RAY DIFFRACTIONr_mcbond_it0.5391.54970
X-RAY DIFFRACTIONr_mcangle_it1.05528044
X-RAY DIFFRACTIONr_scbond_it1.49833558
X-RAY DIFFRACTIONr_scangle_it2.5374.53554
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 181 -
Rwork0.257 3315 -
all-3496 -
obs--86.9 %

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