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- PDB-4r3p: Crystal structures of EGFR in complex with Mig6 -

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Basic information

Entry
Database: PDB / ID: 4r3p
TitleCrystal structures of EGFR in complex with Mig6
Components
  • Epidermal growth factor receptor
  • peptide from ERBB receptor feedback inhibitor 1
KeywordsTRANSFERASE / Kinase / Mig6 / phosphorylation
Function / homology
Function and homology information


response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / negative regulation of protein autophosphorylation / regulation of keratinocyte differentiation / lung epithelium development / chondrocyte proliferation / lung vasculature development / bile acid biosynthetic process ...response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / negative regulation of protein autophosphorylation / regulation of keratinocyte differentiation / lung epithelium development / chondrocyte proliferation / lung vasculature development / bile acid biosynthetic process / skin morphogenesis / tissue homeostasis / positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / Shc-EGFR complex / cartilage development / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / regulation of peptidyl-tyrosine phosphorylation / response to UV-A / tongue development / fat pad development / PLCG1 events in ERBB2 signaling / midgut development / ERBB2-EGFR signaling pathway / digestive tract morphogenesis / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / lung alveolus development / Signaling by EGFR / intracellular vesicle / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / MAP kinase kinase kinase activity / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / positive regulation of bone resorption / embryonic placenta development / positive regulation of phosphorylation / salivary gland morphogenesis / progesterone receptor signaling pathway / peptidyl-tyrosine autophosphorylation / positive regulation of peptidyl-serine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / embryo implantation / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / cholesterol metabolic process / positive regulation of synaptic transmission, glutamatergic / GTPase activator activity / ossification / positive regulation of DNA repair / neuron projection morphogenesis / cholesterol homeostasis / liver development / positive regulation of superoxide anion generation / response to progesterone / positive regulation of epithelial cell proliferation / liver regeneration / epithelial cell proliferation / basal plasma membrane / protein localization to plasma membrane / Signal transduction by L1 / positive regulation of DNA replication / positive regulation of protein localization to plasma membrane / astrocyte activation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to insulin / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Resolution: 2.905 Å
AuthorsPark, E. / Kim, N. / Yi, Z. / Cho, A. / Kim, K. / Ficarro, S.B. / Park, A. / Park, W.Y. / Murray, B. / Meyerson, M. ...Park, E. / Kim, N. / Yi, Z. / Cho, A. / Kim, K. / Ficarro, S.B. / Park, A. / Park, W.Y. / Murray, B. / Meyerson, M. / Beroukim, R. / Marto, J.A. / Cho, J. / Eck, M.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6.
Authors: Park, E. / Kim, N. / Ficarro, S.B. / Zhang, Y. / Lee, B.I. / Cho, A. / Kim, K. / Park, A.K. / Park, W.Y. / Murray, B. / Meyerson, M. / Beroukhim, R. / Marto, J.A. / Cho, J. / Eck, M.J.
History
DepositionAug 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor
B: peptide from ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)37,9252
Polymers37,9252
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.828, 143.828, 143.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1140-

HOH

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Components

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


Mass: 36937.742 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 696-1018) / Mutation: L858R
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) / Strain (production host): SF9
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Protein/peptide peptide from ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein / MIG-6


Mass: 987.023 Da / Num. of mol.: 1 / Fragment: segment 2 (UNP residues 392-398) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJM3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% PEG400, 0.15M Sodium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→45.482 Å / Num. all: 11018 / Num. obs: 11009 / % possible obs: 99.2 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 7 / Biso Wilson estimate: 85.7 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9046-3.03671100
3.0367-3.19681100
3.1968-3.65921100
3.6592-4.02731100
4.0273-4.6095199
4.6095-45.488197

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.905→45.482 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1097 9.96 %
Rwork0.2078 --
obs0.211 11009 99.23 %
all-11018 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.905→45.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 0 54 2559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042559
X-RAY DIFFRACTIONf_angle_d0.8843470
X-RAY DIFFRACTIONf_dihedral_angle_d16.369951
X-RAY DIFFRACTIONf_chiral_restr0.034391
X-RAY DIFFRACTIONf_plane_restr0.004437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9046-3.03670.36821380.3211253X-RAY DIFFRACTION100
3.0367-3.19680.37631340.29971214X-RAY DIFFRACTION100
3.1968-3.3970.31621340.25581236X-RAY DIFFRACTION100
3.397-3.65920.25641370.24291238X-RAY DIFFRACTION100
3.6592-4.02730.24411370.19491221X-RAY DIFFRACTION100
4.0273-4.60950.20071360.18081257X-RAY DIFFRACTION99
4.6095-5.80560.22471350.19451243X-RAY DIFFRACTION99
5.8056-45.4880.21031460.18561250X-RAY DIFFRACTION97

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