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- PDB-7len: Crystal structure of the epidermal growth factor receptor extrace... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7len | ||||||
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Title | Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with trehalose | ||||||
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![]() | SIGNALING PROTEIN / receptor / epiregulin / glioblastoma / cancer / mutation / extracellular / asymmetric / dimer / ErbB1 / EGFR | ||||||
Function / homology | ![]() luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / positive regulation of innate immune response ...luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / positive regulation of innate immune response / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / mRNA transcription / Shc-EGFR complex / ovulation cycle / oocyte maturation / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / epidermal growth factor receptor binding / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / positive regulation of cell division / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / keratinocyte proliferation / negative regulation of mitotic cell cycle / hair follicle development / SHC1 events in ERBB4 signaling / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of protein kinase activity / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / anatomical structure morphogenesis / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / Nuclear signaling by ERBB4 / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / keratinocyte differentiation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of mitotic nuclear division / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / positive regulation of cytokine production / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, C. / Leche II, C.A. / Stayrook, S.E. / Ferguson, K.M. / Lemmon, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Glioblastoma mutations alter EGFR dimer structure to prevent ligand bias. Authors: Hu, C. / Leche 2nd, C.A. / Kiyatkin, A. / Yu, Z. / Stayrook, S.E. / Ferguson, K.M. / Lemmon, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.4 KB | Display | ![]() |
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PDB format | ![]() | 177.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lfrC ![]() 7lfsC ![]() 5wb7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 56494.184 Da / Num. of mol.: 2 / Mutation: R84K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, receptor protein-tyrosine kinase #2: Protein/peptide | Mass: 5480.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 5 types, 7 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020 / Details: Undulator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→43.48 Å / Num. obs: 30250 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.056 / Rrim(I) all: 0.146 / Rsym value: 0.134 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.349 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4148 / CC1/2: 0.489 / Rpim(I) all: 0.572 / Rrim(I) all: 1.467 / Rsym value: 1.349 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WB7 Resolution: 2.9→43.48 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.46 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.53 Å2 / Biso mean: 86.6232 Å2 / Biso min: 35.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→43.48 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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