+Open data
-Basic information
Entry | Database: PDB / ID: 6yoo | ||||||
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Title | Structure of SAMM50 LIR bound to GABARAPL1 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / LIR / SAMM50 / ATG8 | ||||||
Function / homology | Function and homology information MIB complex / SAM complex / inner mitochondrial membrane organization / Cristae formation / mitochondrial respiratory chain complex assembly / glycophagy / cristae formation / Tat protein binding / GABA receptor binding / Mitochondrial protein import ...MIB complex / SAM complex / inner mitochondrial membrane organization / Cristae formation / mitochondrial respiratory chain complex assembly / glycophagy / cristae formation / Tat protein binding / GABA receptor binding / Mitochondrial protein import / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein insertion into mitochondrial outer membrane / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / RAC2 GTPase cycle / cytoplasmic vesicle membrane / phospholipid binding / microtubule / mitochondrial outer membrane / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / extracellular exosome / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | ||||||
Authors | Mouilleron, S. / Wenxin, Z. / Johansen, T. / Tooze, S. / Abudu, Y.P. / Lamark, T. | ||||||
Citation | Journal: To Be Published Title: Structure of SAMM50 LIR bound to GABARAPL1 Authors: Mouilleron, S. / Wenxin, Z. / Johansen, T. / Tooze, S. / Abudu, Y.P. / Lamark, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yoo.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yoo.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 6yoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/6yoo ftp://data.pdbj.org/pub/pdb/validation_reports/yo/6yoo | HTTPS FTP |
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-Related structure data
Related structure data | 6hoiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 14598.667 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: 1377.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMM50, SAM50, CGI-51, TRG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y512 |
-Non-polymers , 4 types, 160 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 24% w/v PEG 6000, 10 mM ZnCl2 and 0.1 M Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→40.76 Å / Num. obs: 825136 / % possible obs: 99.4 % / Redundancy: 12.2 % / Biso Wilson estimate: 11.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.01 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.06→1.1 Å / Rmerge(I) obs: 2.5 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 72954 / CC1/2: 0.62 / Rpim(I) all: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HOI Resolution: 1.06→40.76 Å / SU ML: 0.0637 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7824
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→40.76 Å
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Refine LS restraints |
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LS refinement shell |
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