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- PDB-2jqr: Solution model of crosslinked complex of cytochrome c and adrenodoxin -

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Basic information

Entry
Database: PDB / ID: 2jqr
TitleSolution model of crosslinked complex of cytochrome c and adrenodoxin
Components
  • Adrenodoxin, mitochondrialAdrenal ferredoxin
  • Cytochrome c iso-1
KeywordsELECTRON TRANSPORT / Cytochrome c / Adrenodoxin / Crosslinked complex / 2Fe2S Ferredoxin / Pseudocontact shift / Paramagnetic relaxation enhancement / encounter complex
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / steroid biosynthetic process / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / electron transport chain / respirasome / cellular response to forskolin / cellular response to cAMP / cholesterol metabolic process / respiratory electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / heme binding / protein homodimerization activity / mitochondrion / metal ion binding
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Cytochrome c, class IA/ IB / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Beta-grasp domain superfamily ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Cytochrome c, class IA/ IB / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / 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 c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / Cytochrome c isoform 1 / Adrenodoxin, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (cattle)
MethodSOLUTION NMR / molecular dynamics
AuthorsXu, X. / Reinle, W. / Hannemann, F. / Konarev, P.V. / Svergun, D.I. / Bernhardt, R. / Ubbink, M.
Citation
Journal: J.Am.Chem.Soc. / Year: 2008
Title: Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy
Authors: Xu, X. / Reinle, W. / Hannemann, F. / Konarev, P.V. / Svergun, D.I. / Bernhardt, R. / Ubbink, M.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: High-resolution refinement of yeast iso-1-cytochrome C and comparisons with other eukaryotic cytochromes C
Authors: Louie, G.V. / Brayer, G.D.
#2: Journal: Structure / Year: 1998
Title: New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108)
Authors: Muller, A. / Muller, J.J. / Muller, Y.A. / Uhlmann, H. / Bernhardt, R. / Heinemann, U.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
B: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5054
Polymers23,7112
Non-polymers7942
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c iso-1


Mass: 12075.808 Da / Num. of mol.: 1 / Mutation: V28C, C102T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00044
#2: Protein Adrenodoxin, mitochondrial / Adrenal ferredoxin / Adrenal ferredoxin / Ferredoxin- 1 / Hepato-ferredoxin


Mass: 11635.125 Da / Num. of mol.: 1 / Fragment: 2Fe-2S ferredoxin-type domain, residues 62-166 / Mutation: L80C, C95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: FDX1, ADX / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00257
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
2513D 1H-15N NOESY
2623D 1H-15N NOESY
2743D 1H-15N NOESY
2843D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-98% 15N] CcV28C, 0.2-0.6 mM AdxL80C, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
20.4 mM [U-98% 15N] AdxL80C, 0.2-0.6 mM CcV28C, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
31.0 mM [U-98% 15N] CcV28C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
40.6 mM [U-98% 15N] AdxL80C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMCcV28C[U-98% 15N]1
0.2 mMAdxL80C1
20 mMpotassium phosphate1
0.2 mMAdxL80C[U-98% 15N]2
0.2 mMCcV28C2
20 mMpotassium phosphate2
1.0 mMCcV28C[U-98% 15N]3
5 mMDTT3
20 mMpotassium phosphate3
0.5 mMAdxL80C[U-98% 15N]4
5 mMDTT4
20 mMpotassium phosphate4
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)Ionic strength
17.4 ambient 285 K
27.4 ambient 301 K0.4

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AzaraBoucherprocessing
ANSIGKraulisdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: All structure models are from rigid body modeling. The coordinate of Cytochrome C (Chain A) is from PDB entry 1YCC. All complex structure models are superimposed with Chain A.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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