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Yorodumi- PDB-8d3g: Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d3g | ||||||||||||
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Title | Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A mutant complexed with 6-chloroquinolin-4-amine | ||||||||||||
Components | Apoptosis-inducing factor 1, mitochondrial | ||||||||||||
Keywords | OXIDOREDUCTASE / mitochondrial import / oxidative phosphorylation / SAXS | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / chromosome condensation / cellular response to nitric oxide ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / chromosome condensation / cellular response to nitric oxide / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitochondrial respiratory chain complex I assembly / cellular response to estradiol stimulus / FAD binding / response to ischemia / neuron differentiation / mitochondrial intermembrane space / response to toxic substance / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to hydrogen peroxide / positive regulation of neuron apoptotic process / cellular response to hypoxia / neuron apoptotic process / protein dimerization activity / mitochondrial inner membrane / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||||||||
Authors | Brosey, C.A. / Tainer, J.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat.Chem.Biol. / Year: 2024 Title: Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Authors: Brosey, C.A. / Link, T.M. / Shen, R. / Moiani, D. / Burnett, K. / Hura, G.L. / Jones, D.E. / Tainer, J.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d3g.cif.gz | 582.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d3g.ent.gz | 400.1 KB | Display | PDB format |
PDBx/mmJSON format | 8d3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/8d3g ftp://data.pdbj.org/pub/pdb/validation_reports/d3/8d3g | HTTPS FTP |
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-Related structure data
Related structure data | 8d3eC 8d3hC 8d3iC 8d3jC 8d3kC 8d3nC 8d3oC 5kvhS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.551158083784, -0.00681206366614, -0.834373035559), (0.0370976666442, -0.999177917358, -0.0163478620381), (-0.833575749293, -0.039963549045, 0.550957697957)Vector: - ...NCS oper: (Code: given Matrix: (-0.551158083784, -0.00681206366614, -0.834373035559), Vector: |
-Components
#1: Protein | Mass: 59371.434 Da / Num. of mol.: 2 / Mutation: W196A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: O95831, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 0.3 M Na2SO4, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→29.43 Å / Num. obs: 36184 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 52.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Rrim(I) all: 0.112 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.58→2.69 Å / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 3 / Num. unique obs: 4252 / CC1/2: 0.871 / Rpim(I) all: 0.256 / Rrim(I) all: 0.818 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KVH Resolution: 2.58→29.33 Å / SU ML: 0.3236 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7534 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→29.33 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.474271459623 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1
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