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- PDB-2n18: Dominant form of the low-affinity complex of yeast cytochrome c a... -
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Basic information
Entry | Database: PDB / ID: 2n18 | ||||||
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Title | Dominant form of the low-affinity complex of yeast cytochrome c and cytochrome c peroxidase | ||||||
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![]() | OXIDOREDUCTASE/ELECTRON TRANSPORT / cytochrome c / cytochrome c peroxidase / low affinity complex / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Volkov, A. / Van de Water, K. | ||||||
![]() | ![]() Title: The low-affinity complex of cytochrome c and its peroxidase. Authors: Van de Water, K. / Sterckx, Y.G. / Volkov, A.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDB format | ![]() | 2.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 677.9 KB | Display | ![]() |
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Full document | ![]() | 767.4 KB | Display | |
Data in XML | ![]() | 184.9 KB | Display | |
Data in CIF | ![]() | 245.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data | |
Other databases |
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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: 33543.188 Da / Num. of mol.: 1 / Fragment: UNP residues 68-361 / Mutation: C128A, V197C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Plasmid: pET24 / Production host: ![]() ![]() |
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#2: Protein | Mass: 12073.835 Da / Num. of mol.: 1 / Fragment: UNP residues 3-109 / Mutation: A81C, C102T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Plasmid: pUCcc / Production host: ![]() ![]() |
#3: Protein | Mass: 12073.835 Da / Num. of mol.: 1 / Fragment: UNP residues 2-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Plasmid: pUCcc / Production host: ![]() ![]() |
#4: Chemical | ChemComp-HEM / |
#5: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 1H-15N ![]() |
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Sample preparation
Details | Contents: 0.4 mM [U-2H; U-15N] CcP, 0.4 mM Cc, 0.4 mM Cc1, 20 mM sodium phosphate, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 15 / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: AUTHORS STATE THAT CCP (CHAIN A) HAS TWO BINDING SITES FOR CC (CHAINS B AND C). ONE OF THE SITES IS BLOCKED BY PREPARING A COVALENT CCP-CC CROSSLINK (CHAINS A-B), WHILE STUDYING THE BINDING ...Details: AUTHORS STATE THAT CCP (CHAIN A) HAS TWO BINDING SITES FOR CC (CHAINS B AND C). ONE OF THE SITES IS BLOCKED BY PREPARING A COVALENT CCP-CC CROSSLINK (CHAINS A-B), WHILE STUDYING THE BINDING OF THE SECOND CC MOLECULE (CHAIN C) TO ANOTHER SITE. THE CROSS-LINKING WAS DONE VIA AN ENGINEERED DISULFIDE BETWEEN CCP V197C AND CC A81C GROUPS (I.E. CHAIN A V197C - CHAIN B A81C). IN ADDITION, THE NATIVE CYS RESIDUES OF BOTH CCP AND CC WERE MUTATED OUT (I.E. CHAIN A C128A AND CHAIN B C102T MUTATIONS). THE CROSSLINK STRUCTURE (CHAINS A-B), TAKEN FROM THE PDB ENTRY 1S6V, WAS KEPT FIXED IN THE NMR RESTRAINT-DRIVEN RIGID-BODY DOCKING OF THE SECOND CC MOLECULE (CHAIN C). RIGID-BODY REFINEMENT PROTOCOL IS DESCRIBED IN DETAIL IN THE MAIN CITATION ASSOCIATED WITH THIS ENTRY. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 15 |