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- PDB-4r3r: Crystal structures of EGFR in complex with Mig6 -

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Basic information

Entry
Database: PDB / ID: 4r3r
TitleCrystal structures of EGFR in complex with Mig6
Components
  • Epidermal growth factor receptor
  • peptide from ERBB receptor feedback inhibitor 1'
KeywordsTRANSFERASE / Kinase / phophorylation / ATP hydrolysis / Mig6 / PHOSPHORYLATION
Function / homology
Function and homology information


regulation of type B pancreatic cell proliferation / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / lung vasculature development / negative regulation of protein autophosphorylation / regulation of keratinocyte differentiation / skin morphogenesis / negative regulation of collagen biosynthetic process / lung alveolus development / cellular hyperosmotic response ...regulation of type B pancreatic cell proliferation / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / lung vasculature development / negative regulation of protein autophosphorylation / regulation of keratinocyte differentiation / skin morphogenesis / negative regulation of collagen biosynthetic process / lung alveolus development / cellular hyperosmotic response / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / cellular response to dexamethasone stimulus / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / epidermal growth factor binding / response to UV-A / regulation of peptidyl-tyrosine phosphorylation / negative regulation of interleukin-1 beta production / negative regulation of cardiac muscle hypertrophy in response to stress / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / PTK6 promotes HIF1A stabilization / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / ERBB2 Regulates Cell Motility / Developmental Lineage of Mammary Gland Myoepithelial Cells / protein insertion into membrane / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / negative regulation of tumor necrosis factor production / cellular response to platelet-derived growth factor stimulus / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / GAB1 signalosome / protein tyrosine kinase activator activity / ossification / positive regulation of G1/S transition of mitotic cell cycle / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / positive regulation of epithelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / positive regulation of fibroblast proliferation / SHC1 events in ERBB2 signaling / cellular response to amino acid stimulus / cellular response to epidermal growth factor stimulus / basal plasma membrane / positive regulation of DNA replication / positive regulation of DNA repair / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signal transduction by L1 / GTPase activator activity / cellular response to estradiol stimulus / positive regulation of protein localization to plasma membrane / negative regulation of protein catabolic process / clathrin-coated endocytic vesicle membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / cell-cell adhesion / Signaling by ERBB2 TMD/JMD mutants / negative regulation of ERK1 and ERK2 cascade / EGFR downregulation / Constitutive Signaling by EGFRvIII / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / SH3 domain binding / positive regulation of miRNA transcription / positive regulation of protein phosphorylation / cell junction / epidermal growth factor receptor signaling pathway / kinase binding / ruffle membrane / small GTPase binding / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / HCMV Early Events / positive regulation of canonical Wnt signaling pathway / actin filament binding / cellular response to insulin stimulus / PIP3 activates AKT signaling / neuron differentiation / transmembrane signaling receptor activity / positive regulation of cell growth / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / nuclear membrane / ATPase binding
Similarity search - Function
Cdc42 binding domain-like / : / GTPase binding / : / 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 ...Cdc42 binding domain-like / : / GTPase binding / : / 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 / 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: 3.25 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

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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)38,0052
Polymers38,0052
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-12 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.689, 144.689, 144.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 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, Erbb1(EGFR), 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'


Mass: 1067.002 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.: 49 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
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: 3.26→50 Å / Num. obs: 7110 / % possible obs: 87.75 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 82.7 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.25-3.5192
3.5-3.85191
3.85-4.41189
4.41-5.55186
5.55-45.75182

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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: 3.25→45.755 Å / SU ML: 0.42 / σ(F): 1.36 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 725 10.2 %
Rwork0.1958 --
obs0.2009 7110 87.75 %
all-8107 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→45.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 0 49 2561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052565
X-RAY DIFFRACTIONf_angle_d0.9473476
X-RAY DIFFRACTIONf_dihedral_angle_d14.037957
X-RAY DIFFRACTIONf_chiral_restr0.041390
X-RAY DIFFRACTIONf_plane_restr0.004436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.50090.30811430.27731308X-RAY DIFFRACTION92
3.5009-3.8530.25091490.21461313X-RAY DIFFRACTION91
3.853-4.41010.22871420.19231282X-RAY DIFFRACTION89
4.4101-5.55480.2431480.17451252X-RAY DIFFRACTION86
5.5548-45.75920.24041430.18151230X-RAY DIFFRACTION82
Refinement TLS params.Method: refined / Origin x: -57.0304 Å / Origin y: -8.2123 Å / Origin z: -25.178 Å
111213212223313233
T0.4863 Å2-0.0043 Å20.0042 Å2-0.4768 Å20.0053 Å2--0.3905 Å2
L0.96 °20.6114 °2-0.5994 °2-1.5886 °2-0.9442 °2--0.8524 °2
S-0.0341 Å °-0.0658 Å °-0.0071 Å °-0.1311 Å °-0.0966 Å °-0.1453 Å °0.0275 Å °0.1767 Å °0 Å °
Refinement TLS groupSelection details: all

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