+Open data
-Basic information
Entry | Database: PDB / ID: 7yka | ||||||||||||
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Title | Crystal structure of Fis1 (Mitochondrial fission 1 protein) | ||||||||||||
Components |
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Keywords | APOPTOSIS | ||||||||||||
Function / homology | Function and homology information negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / positive regulation of mitochondrial calcium ion concentration / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / autophagy of mitochondrion / protein targeting to mitochondrion / mitochondrial fission ...negative regulation of fatty acid transport / negative regulation of ATP metabolic process / Class I peroxisomal membrane protein import / positive regulation of mitochondrial calcium ion concentration / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / autophagy of mitochondrion / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / regulation of mitochondrion organization / mitochondrial fusion / positive regulation of mitochondrial fission / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / positive regulation of protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway / mitochondrion organization / release of cytochrome c from mitochondria / peroxisome / positive regulation of cytosolic calcium ion concentration / mitochondrial outer membrane / molecular adaptor activity / lipid binding / endoplasmic reticulum / protein-containing complex / mitochondrion / membrane / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Duc, N.M. / Bong, S.M. / Lee, B.I. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: To Be Published Title: Insight into the Mitochondria-ER tethering revealed by the crystal structure of Fis1-Bap31 complex Authors: Duc, N.M. / Bong, S.M. / Lee, B.I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yka.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yka.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/7yka ftp://data.pdbj.org/pub/pdb/validation_reports/yk/7yka | HTTPS FTP |
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-Related structure data
Related structure data | 7ya9C 1nznS 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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-Components
#1: Protein | Mass: 13803.808 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FIS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6 | ||||
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#2: Protein | Mass: 14218.286 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3D6 | ||||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 100 mM Imidazole pH 8.0 200 mM Zinc acetate 20% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 12419 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 29.47 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 830 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NZN Resolution: 2.3→39.75 Å / SU ML: 0.2958 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.9037 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: 39.34 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.75 Å
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Refine LS restraints |
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LS refinement shell |
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