+Open data
-Basic information
Entry | Database: PDB / ID: 8yfl | ||||||
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Title | crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123 | ||||||
Components |
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Keywords | PROTEIN BINDING / phosphorylation / selective mitophagy | ||||||
Function / homology | Function and homology information regulation of protein lipidation / ribophagy / Atg1/ULK1 kinase complex / glycophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane ...regulation of protein lipidation / ribophagy / Atg1/ULK1 kinase complex / glycophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane / positive regulation of cell size / autophagosome assembly / positive regulation of autophagy / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / autophagy / heart development / nuclear membrane / molecular adaptor activity / lysosome / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Lv, M.Q. / Wu, S.M. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Structural basis for TNIP1 binding to FIP200 during mitophagy. Authors: Wu, S. / Li, M. / Wang, L. / Yang, L. / Cui, J. / Li, F. / Wang, Q. / Shi, Y. / Lv, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yfl.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yfl.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 8yfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yfl_validation.pdf.gz | 479.5 KB | Display | wwPDB validaton report |
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Full document | 8yfl_full_validation.pdf.gz | 480.7 KB | Display | |
Data in XML | 8yfl_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 8yfl_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/8yfl ftp://data.pdbj.org/pub/pdb/validation_reports/yf/8yfl | HTTPS FTP |
-Related structure data
Related structure data | 8yfkC 8yfmC 8yfnC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12039.970 Da / Num. of mol.: 2 / Fragment: claw domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1, KIAA0203, RBICC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDY2 #2: Protein/peptide | Mass: 1288.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | #4: Chemical | ChemComp-MPD / ( | #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: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 15% w/v PEG 6000, 0.1M MES, 5% v/v MPD, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→26.38 Å / Num. obs: 43384 / % possible obs: 99.8 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2076 / CC1/2: 0.966 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→26.38 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→26.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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