+Open data
-Basic information
Entry | Database: PDB / ID: 8x8a | ||||||
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Title | Crystal structure of STBD1 LIR motif in complex with GABARAPL1 | ||||||
Components |
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Keywords | PROTEIN BINDING / STBD1 / LIR / GABARAPL1 | ||||||
Function / homology | Function and homology information substrate localization to autophagosome / glycogen binding / glycophagy / starch binding / Tat protein binding / GABA receptor binding / phagophore assembly site membrane / intracellular transport / phosphatidylethanolamine binding / RHOD GTPase cycle ...substrate localization to autophagosome / glycogen binding / glycophagy / starch binding / Tat protein binding / GABA receptor binding / phagophore assembly site membrane / intracellular transport / phosphatidylethanolamine binding / RHOD GTPase cycle / glycogen catabolic process / autophagy of mitochondrion / cellular response to nitrogen starvation / cargo receptor activity / polysaccharide binding / Macroautophagy / beta-tubulin binding / tertiary granule membrane / autophagosome membrane / ficolin-1-rich granule membrane / autophagosome maturation / autophagosome assembly / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / T-tubule / autophagosome / cytoplasmic vesicle membrane / phospholipid binding / microtubule / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / endoplasmic reticulum / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Zhang, Y.C. / Pan, L.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1. Authors: Zhang, Y. / Sun, Y. / Shi, J. / Xu, P. / Wang, Y. / Liu, J. / Gong, X. / Wang, Y. / Tang, Y. / Liu, H. / Zhou, X. / Lin, Z. / Baba, O. / Morita, T. / Yu, B. / Pan, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x8a.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x8a.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 8x8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x8a_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 8x8a_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 8x8a_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 8x8a_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/8x8a ftp://data.pdbj.org/pub/pdb/validation_reports/x8/8x8a | HTTPS FTP |
-Related structure data
Related structure data | 8x8kC 5lxiS 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: 14068.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8 |
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#2: Protein/peptide | Mass: 2026.129 Da / Num. of mol.: 1 / Fragment: LIR motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STBD1, GENX-3414 / Production host: Escherichia coli (E. coli) / References: UniProt: O95210 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 25% w/v Pentaerythritol Propoxylate (5/4 PO/OH), 0.1 M Sodium acetate pH 4.6, 0.05 M Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.529→50.198 Å / Num. obs: 25598 / % possible obs: 100 % / Redundancy: 38.8 % / Biso Wilson estimate: 26.72 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.529→1.555 Å / Num. unique obs: 25582 / Rpim(I) all: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LXI Resolution: 1.53→25.1 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1097 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: 34.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→25.1 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 | Refine-ID: X-RAY DIFFRACTION
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