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- PDB-3na1: Crystal structure of human CYP11A1 in complex with 20-hydroxychol... -

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Basic information

Entry
Database: PDB / ID: 3na1
TitleCrystal structure of human CYP11A1 in complex with 20-hydroxycholesterol
Components
  • Adrenodoxin, mitochondrial
  • Cholesterol side-chain cleavage enzyme, mitochondrial
KeywordsOxidoreductase / Electron transport / cytochrome P450 / 20-hydroxycholesterol / 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 / cortisol metabolic process / Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / glucocorticoid biosynthetic process / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / Protein lipoylation ...cholesterol monooxygenase (side-chain-cleaving) / cholesterol monooxygenase (side-chain-cleaving) activity / cortisol metabolic process / Electron transport from NADPH to Ferredoxin / Defective CYP11A1 causes AICSR / glucocorticoid biosynthetic process / Mitochondrial iron-sulfur cluster biogenesis / hormone biosynthetic process / P450-containing electron transport chain / Protein lipoylation / sterol metabolic process / C21-steroid hormone biosynthetic process / vitamin D metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cellular response to peptide hormone stimulus / Endogenous sterols / cholesterol metabolic process / cellular response to forskolin / cellular response to cAMP / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / iron ion binding / mitochondrial matrix / 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 / Cytochrome p450 / Cytochrome P450 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. ...: / 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 / Cytochrome p450 / Cytochrome P450 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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
FE2/S2 (INORGANIC) CLUSTER / (3alpha,8alpha)-cholest-5-ene-3,20-diol / 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: 2.25 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
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 1.3Sep 6, 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 / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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, mitochondrial
B: Cholesterol side-chain cleavage enzyme, mitochondrial
C: Adrenodoxin, mitochondrial
D: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,13610
Polymers140,7464
Non-polymers2,3906
Water9,566531
1
A: Cholesterol side-chain cleavage enzyme, mitochondrial
C: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5685
Polymers70,3732
Non-polymers1,1953
Water362
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)71,5685
Polymers70,3732
Non-polymers1,1953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.810, 115.149, 85.727
Angle α, β, γ (deg.)90.00, 101.45, 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, mitochondrial / 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, mitochondrial / Adrenal ferredoxin / Ferredoxin-1 / Hepatoredoxin


Mass: 13488.032 Da / Num. of mol.: 2 / Fragment: UNP residues 62-184
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, 537 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-HCD / (3alpha,8alpha)-cholest-5-ene-3,20-diol / 20S-hydroxycholesterol


Mass: 402.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O2
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
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: 2.25→50 Å / Num. obs: 74265 / % possible obs: 99.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.072 / Χ2: 1.987 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.2940.22335611.9196.2
2.29-2.334.10.20136201.746197.2
2.33-2.384.20.19336641.689197.8
2.38-2.424.30.17836381.757198.4
2.42-2.484.30.1736701.781199.1
2.48-2.534.40.16337041.868199.2
2.53-2.64.40.15337261.732199.6
2.6-2.674.50.14337451.757199.9
2.67-2.754.60.13136891.845199.9
2.75-2.834.60.12137401.8181100
2.83-2.944.70.10837161.9851100
2.94-3.054.70.10137622.0771100
3.05-3.194.70.08837292.3141100
3.19-3.364.70.07437162.2541100
3.36-3.574.70.06137672.0561100
3.57-3.854.70.05137182.0361100
3.85-4.234.70.05137442.476199.9
4.23-4.854.70.04737532.651199.8
4.85-6.14.70.04137641.9941100
6.1-504.60.03138391.788199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3N9Y

3n9y


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.887 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3714 5 %RANDOM
Rwork0.193 ---
obs0.195 73875 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.59 Å2 / Biso mean: 25.989 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-1.34 Å2
2---1.25 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8112 0 152 531 8795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228497
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.98911560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16723.511413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.473151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1021560
X-RAY DIFFRACTIONr_chiral_restr0.0810.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216468
X-RAY DIFFRACTIONr_mcbond_it0.5571.54956
X-RAY DIFFRACTIONr_mcangle_it1.09728021
X-RAY DIFFRACTIONr_scbond_it1.60833541
X-RAY DIFFRACTIONr_scangle_it2.7064.53535
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 250 -
Rwork0.219 5015 -
all-5265 -
obs--95.76 %

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