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- PDB-9by4: Co-crystal structure of the kinase domain of EGFR with non-covale... -

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Basic information

Entry
Database: PDB / ID: 9by4
TitleCo-crystal structure of the kinase domain of EGFR with non-covalent osimertinib
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE / EGFR / kinase domain / ONCOPROTEIN
Function / homology
Function and homology information


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / morphogenesis of an epithelial fold / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / digestive tract morphogenesis / epidermal growth factor binding ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / morphogenesis of an epithelial fold / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / digestive tract morphogenesis / epidermal growth factor binding / response to UV-A / regulation of peptidyl-tyrosine phosphorylation / ubiquitin-dependent endocytosis / PLCG1 events in ERBB2 signaling / cerebral cortex cell migration / ERBB2-EGFR signaling pathway / PTK6 promotes HIF1A stabilization / eyelid development in camera-type eye / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / hair follicle development / intracellular vesicle / ERBB2 Regulates Cell Motility / Developmental Lineage of Mammary Gland Myoepithelial Cells / embryonic placenta development / negative regulation of epidermal growth factor receptor signaling pathway / protein insertion into membrane / protein tyrosine kinase activator activity / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / epithelial cell proliferation / GAB1 signalosome / xenobiotic transport / salivary gland morphogenesis / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / ossification / positive regulation of epithelial cell proliferation / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / basal plasma membrane / positive regulation of DNA replication / positive regulation of DNA repair / cellular response to amino acid stimulus / Signal transduction by L1 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / sperm end piece / positive regulation of protein localization to plasma membrane / cellular response to estradiol stimulus / sperm principal piece / NOTCH3 Activation and Transmission of Signal to the Nucleus / clathrin-coated endocytic vesicle membrane / negative regulation of protein catabolic process / cell-cell adhesion / Signaling by ERBB2 TMD/JMD mutants / EGFR downregulation / Constitutive Signaling by EGFRvIII / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / cell morphogenesis / Signaling by ERBB2 KD Mutants / positive regulation of protein phosphorylation / positive regulation of miRNA transcription / positive regulation of fibroblast proliferation / epidermal growth factor receptor signaling pathway / cell junction / ruffle membrane / kinase binding / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / neuron differentiation / HCMV Early Events / positive regulation of canonical Wnt signaling pathway / gene expression / actin filament binding / transmembrane signaling receptor activity / PIP3 activates AKT signaling / Cargo recognition for clathrin-mediated endocytosis / sperm midpiece / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / virus receptor activity / positive regulation of cell growth / RAF/MAP kinase cascade / nuclear membrane / protein tyrosine kinase activity
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
1,3-PROPANDIOL / Chem-Q6K / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 Å
AuthorsAshtekar, K.D. / Stayrook, S.E. / Lemmon, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GR110199 United States
CitationJournal: To Be Published
Title: Comprehensive characterization of EGFR-tyrosine kinase inhibitor interactions probed by hydrogen-deuterium exchange and mass spectrometry (HDX-MS)
Authors: Tsutsui, Y. / Ashtekar, K.D. / Stayrook, S. / Lemmon, M.A.
History
DepositionMay 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_redundancy / _reflns_shell.pdbx_redundancy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4076
Polymers38,6371
Non-polymers7705
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.968, 145.968, 145.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 38636.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#3: Chemical ChemComp-Q6K / ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide


Mass: 501.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N7O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 67 % / Description: cubic
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, pH 6.0, 0.8 M sodium citrate / PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→103.2 Å / Num. obs: 22884 / % possible obs: 99.9 % / Redundancy: 16.4 % / CC1/2: 0.986 / Net I/σ(I): 18.5
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 16.1 % / Num. unique obs: 2794 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.307→46.159 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1145 5 %
Rwork0.1956 21739 -
obs0.1968 22884 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.04 Å2 / Biso mean: 88.566 Å2 / Biso min: 47.5 Å2
Refinement stepCycle: final / Resolution: 2.307→46.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 53 65 2643
Biso mean--95.55 82.53 -
Num. residues----316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.307-2.41180.3611560.3198263899
2.4118-2.53890.32511620.2782687100
2.5389-2.6980.31361570.25172677100
2.698-2.90630.29661170.24632716100
2.9063-3.19870.30221310.24712729100
3.1987-3.66140.24951460.21532727100
3.6614-4.61230.17721190.16142754100
4.6123-46.1590.18241570.17372811100
Refinement TLS params.Method: refined / Origin x: 58.6151 Å / Origin y: -7.8689 Å / Origin z: 24.8199 Å
111213212223313233
T0.4852 Å2-0.001 Å20.0244 Å2-0.6358 Å2-0.0687 Å2--0.5426 Å2
L1.2205 °2-1.0622 °2-0.7804 °2-3.3348 °21.3287 °2--1.8431 °2
S-0.0778 Å °0.0982 Å °-0.0706 Å °0.2106 Å °-0.187 Å °0.3104 Å °0.1043 Å °-0.3592 Å °0.0002 Å °
Refinement TLS groupSelection details: (chain A and resseq 695:1010)

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