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- PDB-2gs6: Crystal Structure of the active EGFR kinase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2gs6
TitleCrystal Structure of the active EGFR kinase domain in complex with an ATP analog-peptide conjugate
Components
  • Epidermal growth factor receptor
  • Peptide
KeywordsTRANSFERASE / EGFR / kinase / active / ATP-analog peptide conjugate
Function / homology
Function and homology information


: / : / : / positive regulation of miRNA processing / cellular response to xenobiotic stimulus => GO:0071466 / negative regulation of ERBB signaling pathway / magnesium ion homeostasis / ERBB2 signaling pathway / clathrin-coated vesicle membrane / multicellular organism development ...: / : / : / positive regulation of miRNA processing / cellular response to xenobiotic stimulus => GO:0071466 / negative regulation of ERBB signaling pathway / magnesium ion homeostasis / ERBB2 signaling pathway / clathrin-coated vesicle membrane / multicellular organism development / membrane organization / regulation of cell motility / positive regulation of kinase 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 / response to osmotic stress / 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 / regulation of nitric-oxide synthase activity / ERBB2 Activates PTK6 Signaling / morphogenesis of an epithelial fold / intracellular vesicle / Signaling by EGFR / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of Notch signaling pathway / protein insertion into membrane / eyelid development in camera-type eye / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / plasma membrane => GO:0005886 / regulation of JNK cascade / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / endocytic vesicle / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / positive regulation of bone resorption / positive regulation of DNA replication / GAB1 signalosome / positive regulation of nitric oxide mediated signal transduction / salivary gland morphogenesis / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / neurogenesis / cellular response to dexamethasone stimulus / SHC1 events in ERBB2 signaling / ossification / positive regulation of synaptic transmission, glutamatergic / basal plasma membrane / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / positive regulation of superoxide anion generation / Signal transduction by L1 / epithelial cell proliferation / cellular response to estradiol stimulus / liver regeneration / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / cellular response to amino acid stimulus
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-112 / Epidermal growth factor receptor / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, X. / Gureasko, J. / Shen, K. / Cole, P.A. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: An Allosteric Mechanism for Activation of the Kinase Domain of Epidermal Growth Factor Receptor
Authors: Zhang, X. / Gureasko, J. / Shen, K. / Cole, P.A. / Kuriyan, J.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor
B: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7244
Polymers39,1082
Non-polymers6162
Water1,33374
1
A: Epidermal growth factor receptor
B: Peptide
hetero molecules

A: Epidermal growth factor receptor
B: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4488
Polymers78,2164
Non-polymers1,2324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation20_645-z+3/2,x-1/2,-y+1/21
Unit cell
Length a, b, c (Å)144.182, 144.182, 144.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsThe biological assembly is an asymmetric dimer that is generated by a 3(2) fold operation of the monomer in the asymmetric unit: -z+3/2,x-1/2,-y+1/2

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Components

#1: Protein Epidermal growth factor receptor / / Receptor tyrosine-protein kinase ErbB-1


Mass: 37563.457 Da / Num. of mol.: 1 / Fragment: kinase domain, residues 696-1022
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Plasmid: pFASTBAC-HT / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q9H2C9, UniProt: P00533*PLUS, receptor protein-tyrosine kinase
#2: Protein/peptide Peptide /


Mass: 1544.657 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-112 / THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER


Mass: 580.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N6O13P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 18% PEG3350, 0.2 M LiCitrate, 4% Polypropropylene Glycol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15419 / Num. obs: 15419 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rsym value: 0.147 / Net I/σ(I): 28.5
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.46 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
BOSdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M14

1m14


Resolution: 2.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1486 9.6 %random
Rwork0.206 ---
all0.234 14724 --
obs0.234 14724 95.1 %-
Solvent computationBsol: 41.326 Å2
Displacement parametersBiso mean: 35.087 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 36 74 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4361.5
X-RAY DIFFRACTIONc_scbond_it2.0442
X-RAY DIFFRACTIONc_mcangle_it2.5132
X-RAY DIFFRACTIONc_scangle_it3.1352.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ATP_linker_par.txt

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