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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 | ||||||
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Title | Solution model of crosslinked complex of cytochrome c and adrenodoxin | ||||||
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![]() | ELECTRON TRANSPORT / Cytochrome c / Adrenodoxin / Crosslinked complex / 2Fe2S Ferredoxin / Pseudocontact shift / Paramagnetic relaxation enhancement / encounter complex | ||||||
Function / homology | ![]() Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / steroid biosynthetic process / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / respiratory electron transport chain / cholesterol metabolic process / 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 | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
![]() | Xu, X. / Reinle, W. / Hannemann, F. / Konarev, P.V. / Svergun, D.I. / Bernhardt, R. / Ubbink, M. | ||||||
![]() | ![]() Title: Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy. Authors: Xingfu Xu / Wolfgang Reinle / Frank Hannemann / Peter V Konarev / Dmitri I Svergun / Rita Bernhardt / Marcellus Ubbink / ![]() Abstract: In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the ...In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population of the complex. The redox proteins adrenodoxin (Adx) and cytochrome c (C c) associate to form such a weak and short-lived complex, which is nevertheless active in electron transfer. To study the conformational freedom within the protein complex, the native complex has been compared to a cross-linked counterpart by using solution scattering and NMR spectroscopy. Oligomerization behavior of the native complex in solution revealed by small-angle X-ray scattering indicates a stochastic nature of complex formation. For the cross-linked complex, interprotein paramagnetic effects are observed, whereas for the native complex, extensive averaging occurs, consistent with multiple orientations of the proteins within the complex. Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex. #1: ![]() 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: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 659.2 KB | Display | ![]() |
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PDB format | ![]() | 549.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 489.5 KB | Display | ![]() |
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Full document | ![]() | 579.7 KB | Display | |
Data in XML | ![]() | 54 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 12075.808 Da / Num. of mol.: 1 / Mutation: V28C, C102T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CYC1 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Protein | 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.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-HEC / |
#4: Chemical | ChemComp-FES / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 10 |