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

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Basic information

Entry
Database: PDB / ID: 2rfe
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 / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / lung vasculature development / negative regulation of epidermal growth factor-activated receptor activity / bile acid biosynthetic process ...response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / lung epithelium development / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / lung vasculature development / negative regulation of epidermal growth factor-activated receptor activity / bile acid biosynthetic process / skin morphogenesis / tissue homeostasis / cartilage development / 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 / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / tongue development / PLCG1 events in ERBB2 signaling / fat pad development / midgut development / ERBB2-EGFR signaling pathway / digestive tract morphogenesis / PTK6 promotes HIF1A stabilization / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / lung alveolus development / transmembrane receptor protein tyrosine kinase activator activity / intracellular vesicle / response to cobalamin / eyelid development in camera-type eye / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / 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 / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / GAB1 signalosome / positive regulation of bone resorption / regulation of peptidyl-tyrosine phosphorylation / progesterone receptor signaling pathway / positive regulation of phosphorylation / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / GRB2 events in EGFR signaling / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / SHC1 events in EGFR signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / EGFR Transactivation by Gastrin / embryo implantation / GRB2 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / SHC1 events in ERBB2 signaling / positive regulation of DNA repair / cellular response to dexamethasone stimulus / cholesterol metabolic process / ossification / positive regulation of synaptic transmission, glutamatergic / GTPase activator activity / neuron projection morphogenesis / basal plasma membrane / positive regulation of epithelial cell proliferation / liver development / positive regulation of superoxide anion generation / cholesterol homeostasis / liver regeneration / epithelial cell proliferation / neurogenesis / positive regulation of DNA replication / response to progesterone / Signal transduction by L1 / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / astrocyte activation / NOTCH3 Activation and Transmission of Signal to the Nucleus / epidermal growth factor receptor activity
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 / molecular replacement / Resolution: 2.9 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
Revision 1.3Oct 20, 2021Group: Database references / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Epidermal growth factor receptor
D: Epidermal growth factor receptor
E: ERBB receptor feedback inhibitor 1
F: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)156,3716
Polymers156,3716
Non-polymers00
Water64936
1
A: Epidermal growth factor receptor
E: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers41,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
MethodPISA
2
B: Epidermal growth factor receptor
F: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers41,2192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
MethodPISA
3
C: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)36,9671
Polymers36,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)36,9671
Polymers36,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.508, 98.425, 101.496
Angle α, β, γ (deg.)90.000, 112.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36966.801 Da / Num. of mol.: 4 / Fragment: Protein kinase domain / Mutation: K799E
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/peptide ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein / Mig-6


Mass: 4251.812 Da / Num. of mol.: 2 / Fragment: sequence database residues, 325-364 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJM3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG3350, 100 mM NaNO3, 100 mM Bis-Tris propane, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 32555 / % possible obs: 90.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.082 / Χ2: 1.047 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-31.80.32421030.99458.4
3-3.121.90.32425391.02870.9
3.12-3.271.90.25429701.07182.7
3.27-3.4420.19133481.08793.2
3.44-3.652.10.15635191.05898.3
3.65-3.942.10.10636331.06399.9
3.94-4.332.10.07935871.07599.8
4.33-4.962.10.06336151.0299.5
4.96-6.242.10.06435961.04199.2
6.24-502.10.03136451.01598.1

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GS7

2gs7


Resolution: 2.9→49.85 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1514 4.1 %random
Rwork0.229 ---
obs-30226 82.6 %-
Solvent computationBsol: 32.294 Å2
Displacement parametersBiso mean: 61.158 Å2
Baniso -1Baniso -2Baniso -3
1-27.155 Å20 Å2-13.079 Å2
2--9.424 Å20 Å2
3----36.578 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8853 0 0 36 8889
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3371.5
X-RAY DIFFRACTIONc_scbond_it1.7152
X-RAY DIFFRACTIONc_mcangle_it2.3922
X-RAY DIFFRACTIONc_scangle_it2.8072.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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