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Open data
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Basic information
Entry | Database: PDB / ID: 8s1m | ||||||
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Title | Crystal structure of human GABARAP fused to EGFR (1076-1099) | ||||||
![]() | Epidermal growth factor receptor,Gamma-aminobutyric acid receptor-associated protein | ||||||
![]() | PROTEIN BINDING / Atg8 / Receptor-trafficking | ||||||
Function / homology | ![]() positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / positive regulation of prolactin secretion / Shc-EGFR complex / microtubule associated complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / tongue development / response to UV-A / PLCG1 events in ERBB2 signaling / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / Macroautophagy / digestive tract morphogenesis / Signaling by EGFR / response to cobalamin / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / hepatocyte growth factor receptor activity / platelet-derived growth factor beta-receptor activity / placental growth factor receptor activity / brain-derived neurotrophic factor receptor activity / boss receptor activity / platelet-derived growth factor alpha-receptor activity / epidermal growth factor receptor activity / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / macrophage colony-stimulating factor receptor activity / autophagosome membrane / positive regulation of bone resorption / protein tyrosine kinase collagen receptor activity / stem cell factor receptor activity / Signaling by ERBB4 / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / insulin-like growth factor receptor activity / transmembrane-ephrin receptor activity / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / positive regulation of phosphorylation / autophagosome assembly / positive regulation of peptidyl-serine phosphorylation / autophagosome maturation / GPI-linked ephrin receptor activity / vascular endothelial growth factor receptor activity / peptidyl-tyrosine autophosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / beta-tubulin binding / embryonic placenta development / fibroblast growth factor receptor activity / protein targeting / smooth endoplasmic reticulum / insulin receptor activity / salivary gland morphogenesis / positive regulation of vasoconstriction / mitophagy / sperm midpiece / Signaling by ERBB2 / positive regulation of glial cell proliferation / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / cellular response to dexamethasone stimulus / GRB2 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / SHC1 events in ERBB2 signaling / ossification / autophagosome / basal plasma membrane / positive regulation of DNA repair / cellular response to epidermal growth factor stimulus / positive regulation of epithelial cell proliferation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ueffing, A. / Willbold, D. / Weiergraeber, O.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: GABARAP interacts with EGFR - supporting the unique role of this hAtg8 protein during receptor trafficking. Authors: Uffing, A. / Weiergraber, O.H. / Schwarten, M. / Hoffmann, S. / Willbold, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.3 KB | Display | ![]() |
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PDB format | ![]() | 49.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 354.8 KB | Display | ![]() |
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Full document | ![]() | 396.3 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16905.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: EGFR(1052-1075) fused to N-terminus of GABARAP,EGFR(1052-1075) fused to N-terminus of GABARAP,EGFR(1052-1075) fused to N-terminus of GABARAP,EGFR(1052-1075) fused to N-terminus of GABARAP Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, UniProt: O95166, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.17 M ammonium acetate 0.085 M sodium citrate 25.5% PEG 4000 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→41.35 Å / Num. obs: 11007 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 57.43 Å2 / CC1/2: 1 / Net I/σ(I): 21.91 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 798 / CC1/2: 0.365 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→41.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.4256493167 Å / Origin y: 31.1975939398 Å / Origin z: 2.16098169233 Å
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Refinement TLS group | Selection details: chain 'A' and (resid 1 through 117 ) |