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- PDB-2rf9: Crystal structure of the complex between the EGFR kinase domain a... -

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Basic information

Entry
Database: PDB / ID: 2rf9
TitleCrystal structure of the complex between the EGFR kinase domain and a Mig6 peptide
Components
  • ERBB receptor feedback inhibitor 1
  • Epidermal growth factor receptor
KeywordsTRANSFERASE / kinase domain / inhibition / dimer / Alternative splicing / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Glycoprotein / Membrane / Nucleotide-binding / Phosphorylation / Polymorphism / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase / Ubl conjugation / Cytoplasm
Function / homology
Function and homology information


response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / lung epithelium development / negative regulation of epidermal growth factor-activated receptor activity / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / lung vasculature development / bile acid biosynthetic process ...response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / lung epithelium development / negative regulation of epidermal growth factor-activated receptor activity / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / lung vasculature development / bile acid biosynthetic process / skin morphogenesis / tissue homeostasis / cartilage development / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / 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 / epidermal growth factor binding / response to UV-A / fat pad development / tongue development / PLCG1 events in ERBB2 signaling / midgut development / lung alveolus development / hydrogen peroxide metabolic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ERBB2-EGFR signaling pathway / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / protein tyrosine kinase activator activity / response to cobalamin / Signaling by ERBB4 / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / MAP kinase kinase kinase activity / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / progesterone receptor signaling pathway / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of vasoconstriction / positive regulation of glial cell proliferation / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / embryo implantation / cholesterol metabolic process / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of DNA repair / regulation of ERK1 and ERK2 cascade / SHC1 events in ERBB2 signaling / GTPase activator activity / ossification / cellular response to dexamethasone stimulus / neurogenesis / positive regulation of synaptic transmission, glutamatergic / positive regulation of epithelial cell proliferation / liver development / neuron projection morphogenesis / basal plasma membrane / cholesterol homeostasis / epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / Signal transduction by L1 / protein localization to plasma membrane / cellular response to estradiol stimulus
Similarity search - Function
Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV ...Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Epidermal growth factor receptor / ERBB receptor feedback inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsZhang, X. / Pickin, K.A. / Bose, R. / Jura, N. / Cole, P.A. / Kuriyan, J.
CitationJournal: Nature / Year: 2007
Title: Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface.
Authors: Zhang, X. / Pickin, K.A. / Bose, R. / Jura, N. / Cole, P.A. / Kuriyan, J.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor
B: Epidermal growth factor receptor
C: ERBB receptor feedback inhibitor 1
D: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)88,8604
Polymers88,8604
Non-polymers00
Water00
1
A: Epidermal growth factor receptor
C: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)44,4302
Polymers44,4302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
MethodPISA
2
B: Epidermal growth factor receptor
D: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)44,4302
Polymers44,4302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.762, 42.650, 99.726
Angle α, β, γ (deg.)90.000, 109.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 37563.457 Da / Num. of mol.: 2 / Fragment: Protein kinase domain
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: P00533, receptor protein-tyrosine kinase
#2: Protein ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein / Mig-6


Mass: 6866.682 Da / Num. of mol.: 2 / Fragment: sequence database residues, 315-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERRFI1, MIG6 / Plasmid: pGEX6p1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJM3

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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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG3350, 300 mM KAC, 10% Glycerol and 100 mM NaAc, pH 5.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 9081 / % possible obs: 91.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.147 / Χ2: 1.049 / Net I/σ(I): 6.7
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / Num. unique all: 736 / Χ2: 0.935 / % possible all: 74.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GS7

2gs7


Resolution: 3.5→47.11 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 455 4.6 %Random
Rwork0.272 ---
obs-8319 84.5 %-
Solvent computationBsol: 67.047 Å2
Displacement parametersBiso mean: 68.346 Å2
Baniso -1Baniso -2Baniso -3
1--24.635 Å20 Å2-16.14 Å2
2--0.865 Å20 Å2
3---23.771 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4435 0 0 0 4435
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1761.5
X-RAY DIFFRACTIONc_scbond_it1.4492
X-RAY DIFFRACTIONc_mcangle_it2.1072
X-RAY DIFFRACTIONc_scangle_it2.42.5
Xplor fileSerial no: 1 / Param file: protein_rep.param

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