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- PDB-2jiv: Crystal structure of EGFR kinase domain T790M mutation in compex ... -
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Basic information
Entry | Database: PDB / ID: 2jiv | ||||||
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Title | Crystal structure of EGFR kinase domain T790M mutation in compex with HKI-272 | ||||||
![]() | EPIDERMAL GROWTH FACTOR RECEPTOR | ||||||
![]() | TRANSFERASE / HKI272 / HKI-272 / RECEPTOR / CELL CYCLE / ATP-BINDING / TYROSINE-PROTEIN KINASE / TRANSMEMBRANE / PHOSPHORYLATION / DISEASE MUTATION / NUCLEOTIDE-BINDING / ANTI-ONCOGENE / EPIDERMAL GROWTH FACTOR | ||||||
Function / homology | ![]() 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 / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...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 / Shc-EGFR complex / ovulation cycle / 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 / 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 / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / cellular response to cadmium ion / EGFR Transactivation by Gastrin / 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 synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / positive regulation of superoxide anion generation / epithelial cell proliferation / positive regulation of DNA replication / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / ruffle membrane / positive regulation of miRNA transcription / cell-cell adhesion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yun, C.-H. / Mengwasser, K.E. / Toms, A.V. / Li, Y. / Woo, M.S. / Greulich, H. / Wong, K.-K. / Meyerson, M. / Eck, M.J. | ||||||
![]() | ![]() Title: The T790M Mutation in Egfr Kinase Causes Drug Resistance by Increasing the Affinity for ATP. Authors: Yun, C.-H. / Mengwasser, K.E. / Toms, A.V. / Woo, M.S. / Greulich, H. / Wong, K.-K. / Meyerson, M. / Eck, M.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 47.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jitC ![]() 2jiuC ![]() 2gs7S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.69128, -0.71512, 0.10362), Vector: |
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Components
#1: Protein | Mass: 37421.301 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 695-1022 / Mutation: YES Source method: isolated from a genetically manipulated source Details: EGFR 696-1022 T790M / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, EC: 2.7.1.112, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | RECEPTOR FOR EGF, BUT ALSO FOR OTHER MEMBERS OF THE EGF FAMILY ENGINEERED RESIDUE IN CHAIN A, THR ...RECEPTOR FOR EGF, BUT ALSO FOR OTHER MEMBERS OF THE EGF FAMILY ENGINEERED | Nonpolymer details | CYSTEINE MODIFIED BY HKI-272 (HKI): CYSTEINE RESIDUE COVALENTLY CONNECTS TO HKI-272, A IRREVERSIBLE ...CYSTEINE MODIFIED BY HKI-272 (HKI): CYSTEINE RESIDUE COVALENTLY | Sequence details | T790M MUTATION. CYS797 MODIFIED BY HKI-272 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M HEPES PH7.0, 0.2M LI2SO4, 28% PEG3350, 5MM TCEP, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 28, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 8699 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.5→3.77 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GS7 Resolution: 3.5→25 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.806 / Cross valid method: THROUGHOUT / ESU R Free: 0.772 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STEREO-CHEMISTRY RESTRAINTS ENFORCED DUE TO LOW RESOLUTION OF THE DIFFRACTION DATA.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.59 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→25 Å
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Refine LS restraints |
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