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Yorodumi- PDB-8dzl: Structure of the K39Q mutant of rat somatic Cytochrome c at 1.36A -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dzl | ||||||
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Title | Structure of the K39Q mutant of rat somatic Cytochrome c at 1.36A | ||||||
Components | Cytochrome c, somatic | ||||||
Keywords | ELECTRON TRANSPORT / complex IV / Complex III / apoptosis / ischemia / skeletal muscle / acetylation / oxidoreductase | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 / apoptosome / Regulation of the apoptosome activity / negative regulation of hydrogen peroxide biosynthetic process / response to gravity / positive regulation of cellular respiration / glial cell apoptotic process / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / hydrogen peroxide metabolic process / respirasome / response to ischemia / mitochondrial intermembrane space / response to oxidative stress / electron transfer activity / apoptotic process / heme binding / enzyme binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Edwards, B.F.P. / Huettemann, M. / Vaishnav, A. / Brunzelle, J. / Morse, P. / Wan, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle. Authors: Morse, P.T. / Perez-Mejias, G. / Wan, J. / Turner, A.A. / Marquez, I. / Kalpage, H.A. / Vaishnav, A. / Zurek, M.P. / Huettemann, P.P. / Kim, K. / Arroum, T. / De la Rosa, M.A. / Chowdhury, D. ...Authors: Morse, P.T. / Perez-Mejias, G. / Wan, J. / Turner, A.A. / Marquez, I. / Kalpage, H.A. / Vaishnav, A. / Zurek, M.P. / Huettemann, P.P. / Kim, K. / Arroum, T. / De la Rosa, M.A. / Chowdhury, D.D. / Lee, I. / Brunzelle, J.S. / Sanderson, T.H. / Malek, M.H. / Meierhofer, D. / Edwards, B.F.P. / Diaz-Moreno, I. / Huttemann, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dzl.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dzl.ent.gz | 161.2 KB | Display | PDB format |
PDBx/mmJSON format | 8dzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/8dzl ftp://data.pdbj.org/pub/pdb/validation_reports/dz/8dzl | HTTPS FTP |
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-Related structure data
Related structure data | 8dvxC 5c0zS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 11496.242 Da / Num. of mol.: 4 / Mutation: K39Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cycs / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P62898 #2: Chemical | ChemComp-HEC / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 40.78 % / Description: Red crystals: 0.2 x 0.1 rectanglar bricks |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Wizard Cryo 2#30: 40% PEG 600, 100mM Sodium Citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2022 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→58.1 Å / Num. obs: 83554 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.026 / Rrim(I) all: 0.092 / Χ2: 0.78 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.36→1.43 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12815 / CC1/2: 0.942 / Rpim(I) all: 0.233 / Rrim(I) all: 0.831 / Χ2: 0.45 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C0Z Resolution: 1.36→58.1 Å / SU ML: 0.1159 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.7865 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→58.1 Å
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Refine LS restraints |
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LS refinement shell |
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