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- PDB-5czi: EGFR L858R MUTANT IN COMPLEX WITH A SHC PEPTIDE SUBSTRATE -

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Basic information

Entry
Database: PDB / ID: 5czi
TitleEGFR L858R MUTANT IN COMPLEX WITH A SHC PEPTIDE SUBSTRATE
Components
  • Epidermal growth factor receptor
  • SHC Peptide substrate
KeywordsTRANSFERASE / EGFR / L858R / KINASE / EGF
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / 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 / Interleukin-2 signaling / 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 / 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 / epidermal growth factor receptor binding / morphogenesis of an epithelial fold / Signaling by ALK / ERBB2 Activates PTK6 Signaling / 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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by ERBB4 / protein insertion into membrane / eyelid development in camera-type eye / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / negative regulation of mitotic cell cycle / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / hair follicle development / Interleukin-3, Interleukin-5 and GM-CSF signaling / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / SHC1 events in ERBB4 signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / Signalling to RAS / positive regulation of bone resorption / positive regulation of DNA replication / GAB1 signalosome / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / positive regulation of nitric oxide mediated signal transduction / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / salivary gland morphogenesis / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by CSF3 (G-CSF) / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / Tie2 Signaling / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in EGFR signaling / insulin-like growth factor receptor binding / 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 / neurogenesis / transmembrane receptor protein tyrosine kinase activity / phosphotyrosine residue binding / ephrin receptor binding / cellular response to dexamethasone stimulus / SHC1 events in ERBB2 signaling
Similarity search - Function
Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 ...Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / 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
Epidermal growth factor receptor / SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli H489 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsYun, C.H. / Eck, M.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: EGF-receptor specificity for phosphotyrosine-primed substrates provides signal integration with Src.
Authors: Begley, M.J. / Yun, C.H. / Gewinner, C.A. / Asara, J.M. / Johnson, J.L. / Coyle, A.J. / Eck, M.J. / Apostolou, I. / Cantley, L.C.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor
B: SHC Peptide substrate


Theoretical massNumber of molelcules
Total (without water)38,9562
Polymers38,9562
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.890, 143.890, 143.890
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: 37676.484 Da / Num. of mol.: 1 / Fragment: EGFR UNP RESIDUES 694-1022 / Mutation: YES
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)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Protein/peptide SHC Peptide substrate / SHC-TRANSFORMING PROTEIN 3 / SHC-TRANSFORMING PROTEIN A / SRC HOMOLOGY 2 DOMAIN-CONTAINING- ...SHC-TRANSFORMING PROTEIN 3 / SHC-TRANSFORMING PROTEIN A / SRC HOMOLOGY 2 DOMAIN-CONTAINING-TRANSFORMING PROTEIN C1 / SH2 DOMAIN PROTEIN C1


Mass: 1279.184 Da / Num. of mol.: 1 / Fragment: SHC PEPTIDE UNP RESIDUES 345-353 / Source method: obtained synthetically
Details: THE OPTIMIZED PEPTIDE WAS GENERATED BY LIBRARY SCREENING.
Source: (synth.) Escherichia coli H489 (bacteria) / References: UniProt: P29353*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 61.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1M HEPES 7.6, 0.15M NACL, 40% PEG400, 5MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2011
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15212 / % possible obs: 99 % / Observed criterion σ(I): -3.3 / Redundancy: 3.4 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
PHENIX1.8_1069refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2ITV

2itv


Resolution: 2.6→38.46 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 758 4.98 %
Rwork0.183 --
obs0.185 15207 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 0 129 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012570
X-RAY DIFFRACTIONf_angle_d1.183481
X-RAY DIFFRACTIONf_dihedral_angle_d17.034960
X-RAY DIFFRACTIONf_chiral_restr0.083388
X-RAY DIFFRACTIONf_plane_restr0.006441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6038-2.80480.30891630.2472869X-RAY DIFFRACTION100
2.8048-3.08690.28121600.22562883X-RAY DIFFRACTION100
3.0869-3.53340.26351420.19912869X-RAY DIFFRACTION100
3.5334-4.45060.19741490.1592925X-RAY DIFFRACTION99
4.4506-38.46150.19691440.17212903X-RAY DIFFRACTION97

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