[English] 日本語
Yorodumi
- PDB-1e6e: ADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 S... -

+
Open data


ID or keywords:

Loading...

-
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 / : / 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 ...adrenodoxin-NADP+ reductase / : / 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 / steroid biosynthetic process / cellular response to cAMP / cellular response to forskolin / cholesterol metabolic process / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / NADP binding / electron transfer activity / mitochondrial inner membrane / 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 / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / 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 (domestic 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 (domestic 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 (domestic 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

-
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

-
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.

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more