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- PDB-4i21: Crystal structure of L858R + T790M EGFR kinase domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 4i21
TitleCrystal structure of L858R + T790M EGFR kinase domain in complex with MIG6 peptide
Components
  • ERBB receptor feedback inhibitor 1
  • Epidermal growth factor receptor
KeywordsTransferase/Transferase Inhibitor / EGFR kinase domain / Phosphotransfer / MIG6 peptide / ATP binding / Transferase-Transferase Inhibitor complex
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 / negative regulation of epidermal growth factor receptor signaling pathway / tissue homeostasis / cartilage development / fat pad development / lung alveolus development / progesterone receptor signaling pathway / Complex I biogenesis / Respiratory electron transport / epithelial cell proliferation / embryo implantation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cholesterol metabolic process / GTPase activator activity / liver development / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / cholesterol homeostasis / protein localization to plasma membrane / epidermal growth factor receptor signaling pathway / response to progesterone / NADH dehydrogenase (ubiquinone) activity / response to insulin / aerobic respiration / glucose metabolic process / cell migration / response to estradiol / gene expression / electron transfer activity / mitochondrial inner membrane / response to xenobiotic stimulus / protein kinase binding / apoptotic process / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Zinc finger, CHCC-type / Zinc-finger domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 ...Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Zinc finger, CHCC-type / Zinc-finger domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / ERBB receptor feedback inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsGajiwala, K.S. / Feng, J. / Ferre, R. / Ryan, K. / Brodsky, O. / Stewart, A.
CitationJournal: Structure / Year: 2013
Title: Insights into the Aberrant Activity of Mutant EGFR Kinase Domain and Drug Recognition.
Authors: Gajiwala, K.S. / Feng, J. / Ferre, R. / Ryan, K. / Brodsky, O. / Weinrich, S. / Kath, J.C. / Stewart, A.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: Epidermal growth factor receptor
C: ERBB receptor feedback inhibitor 1
D: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)88,2434
Polymers88,2434
Non-polymers00
Water00
1
A: Epidermal growth factor receptor
C: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)44,1222
Polymers44,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-12 kcal/mol
Surface area16210 Å2
MethodPISA
2
B: Epidermal growth factor receptor
D: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)44,1222
Polymers44,1222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.666, 66.050, 94.518
Angle α, β, γ (deg.)71.85, 87.38, 74.26
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 37522.387 Da / Num. of mol.: 2 / Fragment: UNP residues 695-1022, EGFR kinase domain / Mutation: L858R, T790M
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 ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein / MIG-6


Mass: 6599.357 Da / Num. of mol.: 2 / Fragment: UNP residues 315-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERRFI1, MIG6 / Production host: Escherichia coli (E. coli) / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14.5% PEG 8,000, 0.1M Na Acetate trihydrate pH 4.8-5.5, 0.2-0.38 M K acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
PH range: 4.8 - 5.5

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2011 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.37→42.99 Å / Num. all: 12057 / Num. obs: 11744 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10
Reflection shellResolution: 3.37→3.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1723 / % possible all: 96.9

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Processing

Software
NameClassification
JDirectordata collection
CNXrefinement
autoPROCdata scaling
SCALAdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.37→37.18 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 590966.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 605 5.2 %RANDOM
Rwork0.23 ---
all0.233 11738 --
obs0.233 11738 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8752 Å2 / ksol: 0.325091 e/Å3
Displacement parametersBiso mean: 69.9 Å2
Baniso -1Baniso -2Baniso -3
1-29.54 Å2-9.06 Å211.82 Å2
2---9.66 Å24.83 Å2
3----19.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.37→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 0 0 5182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.652.5
Refine LS restraints NCSWeight Biso : 2 / Weight position: 300
LS refinement shellResolution: 3.37→3.58 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 120 6.2 %
Rwork0.317 1808 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paraprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paradna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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