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- PDB-1e6e: ADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 S... -

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Basic information

Entry
Database: PDB / ID: 1e6e
TitleADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 SYSTEMS
Components
  • ADRENODOXIN
  • NADPH\:ADRENODOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ELECTRON TRANSFERASE / [2FE-2S]FERREDOXIN / ADRENODOXIN / ELECTRON TRANSPORT / COMPLEX
Function / homology
Function and homology information


adrenodoxin-NADP+ reductase / NADPH-adrenodoxin reductase activity / Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / NADPH oxidation ...adrenodoxin-NADP+ reductase / NADPH-adrenodoxin reductase activity / Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / NADPH oxidation / steroid biosynthetic process / cholesterol metabolic process / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / NADP binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / metal ion binding
Similarity search - Function
Ferredoxin-NADP+ reductase, adrenodoxin-type / : / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Beta-grasp domain superfamily ...Ferredoxin-NADP+ reductase, adrenodoxin-type / : / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Adrenodoxin, mitochondrial / NADPH:adrenodoxin oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMueller, J.J. / Lapko, A. / Bourenkov, G. / Ruckpaul, K. / Heinemann, U.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Adrenodoxin Reductase-Adrenodoxin Complex Structure Suggests Electron Transfer Path in Steroid Biosynthesis.
Authors: Mueller, J.J. / Lapko, A. / Bourenkov, G. / Ruckpaul, K. / Heinemann, U.
#1: Journal: To be Published
Title: X-Ray Structure of Bovine Adrenodoxin Reductase -Adrenodoxin Complex at 2.5 A Resolution: The First Three-Dimensional Structure of a Complex of Two Components of the Steroidogenic Electron ...Title: X-Ray Structure of Bovine Adrenodoxin Reductase -Adrenodoxin Complex at 2.5 A Resolution: The First Three-Dimensional Structure of a Complex of Two Components of the Steroidogenic Electron Transport System in Adrenal Cortex Mitochondria
Authors: Mueller, J.J. / Lapko, A. / Bourenkov, G. / Mueller, E.C. / Otto, A. / Ruckpaul, K. / Heinemann, U.
#2: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997
Title: Preparation and Crystallization of a Cross-Linked Complex of Bovine Adrenodoxin and Adrenodoxin Reductase
Authors: Lapko, A. / Mueller, A. / Heese, O. / Ruckpaul, K. / Heinemann, U.
History
DepositionAug 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: NADPH\:ADRENODOXIN OXIDOREDUCTASE
B: ADRENODOXIN
C: NADPH\:ADRENODOXIN OXIDOREDUCTASE
D: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,18713
Polymers128,7844
Non-polymers2,4039
Water4,936274
1
A: NADPH\:ADRENODOXIN OXIDOREDUCTASE
B: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6427
Polymers64,3922
Non-polymers1,2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-57.4 kcal/mol
Surface area24320 Å2
MethodPISA
2
C: NADPH\:ADRENODOXIN OXIDOREDUCTASE
D: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5466
Polymers64,3922
Non-polymers1,1534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-70 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.210, 92.210, 607.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein NADPH\:ADRENODOXIN OXIDOREDUCTASE / AR / ADRENODOXIN REDUCTASE / FERREDOXIN--NADP(+) REDUCTASE FERREDOXIN REDUCTASE / ADR / ADRENODOXIN REDUCTASE


Mass: 50360.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT CROSSLINK BETWEEN LYS27 OF ADR AND ASP39 OF ADX
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: STEROIDOGENIC TISSUES / Cell: MITOCHONDRION / Cellular location: ATTACHED TO INNER MITOCHONDRIAL MEMBRANE / Organ: ADRENAL GLAND / Organelle: MITOCHONDRIAL MATRIX / Plasmid: PBAR1607 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P08165, ferredoxin-NADP+ reductase, adrenodoxin-NADP+ reductase
#2: Protein ADRENODOXIN / ADRENAL FERREDOXIN / FERREDOXIN-1 / HEPATO-FERREDOXIN / ADX / A DRENODOXIN


Mass: 14031.734 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COVALENT CROSSLINK BETWEEN LYS27 OF ADR AND ASP39 OF ADX
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: STEROIDOGENIC TISSUES / Cell: MITOCHONDRION / Organ: ADRENAL GLAND / Organelle: MITOCHONDRIAL MATRIX / Plasmid: PKKHC, PMIXT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00257

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Non-polymers , 4 types, 283 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN B, D ENGINEERED MUTATION SER1GLY REDUCED ADRENODOXIN + NADP(+) = OXIDIZED ADRENODOXIN + NADPH ...CHAIN B, D ENGINEERED MUTATION SER1GLY REDUCED ADRENODOXIN + NADP(+) = OXIDIZED ADRENODOXIN + NADPH THE COVALENT CROSSLINK BETWEEN ASP39CG OF ADX AND LYS27NZ OF ADR WAS MEDIATED BY 1-ETHYL-3-(3-DIMETHYLAMINOPROPYL) CARBODIIMIDE (EDC) ADRENODOXIN TRANSFER ELECTRONS FROM ADRENODOXIN REDUCTASE TO THE CHOLESTEROL SIDE CHAIN CLEAVAGE CYTOCHROME P450
Sequence detailsFIRST 32 RESIDUES OF ADR SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS ...FIRST 32 RESIDUES OF ADR SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS CLEAVED WHEN CLONED. FIRST 58 RESIDUES OF ADX SWISS-PROT PRECURSOR SEQUENCE WERE CLEAVED WHEN CLONED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING DROP VAPOR-DIFFUSION AT 4 DEGR. 0.5MM COMPLEX IN 100MMTRIS-HCL, PH 7.4, 0.9M AMMONIUMSULFATE.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Lapko, A., (1997) Proteins: Struct.,Funct., Genet., 28, 289.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMcomplex1drop
2100 mMTris-HCl1droppH7.4
31.9 Mammonium sulfate1drop
41.9 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.046
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.046 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 55229 / % possible obs: 79.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 18.5
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 11 / Rsym value: 0.11 / % possible all: 56
Reflection
*PLUS
Num. measured all: 201839 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 56 % / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AYF AND 1CJC

1ayf

1cjc


Resolution: 2.3→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4745426 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2791 5.1 %RANDOM
Rwork0.222 ---
obs0.222 55229 79.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.9964 Å2 / ksol: 0.348512 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å24.19 Å20 Å2
2--0.49 Å20 Å2
3----0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 139 274 9112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.244
X-RAY DIFFRACTIONc_mcangle_it2.155
X-RAY DIFFRACTIONc_scbond_it1.829
X-RAY DIFFRACTIONc_scangle_it2.854
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 300 4.7 %
Rwork0.249 6049 -
obs--55.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION2FAD.PARFAD.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.993
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2.3 Å

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