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

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Basic information

Entry
Database: PDB / ID: 2rfd
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 / 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 / molecular replacement / Resolution: 3.6 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 / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4305
Polymers79,3344
Non-polymers961
Water00
1
A: Epidermal growth factor receptor
C: ERBB receptor feedback inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7633
Polymers39,6672
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
MethodPISA
2
B: Epidermal growth factor receptor
D: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)39,6672
Polymers39,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.964, 143.964, 237.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 36966.801 Da / Num. of mol.: 2 / 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: 2700.071 Da / Num. of mol.: 2 / Fragment: sequence database residues, 340-364 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJM3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 200 mM Na2SO4, 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: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 17156 / % possible obs: 98.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.136 / Χ2: 4.586 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.6-3.734.10.45414824.79888.1
3.73-3.885.90.41616805.06798.2
3.88-4.057.40.32116854.77599.4
4.05-4.278.20.23917184.85999.8
4.27-4.548.50.19317145.0399.8
4.54-4.898.50.16217174.53899.5
4.89-5.388.50.15517334.56799.5
5.38-6.158.40.14317564.76999.3
6.15-7.758.10.09717724.6999.1
7.75-507.90.03518993.15897.7

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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: 3.6→49.01 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 798 4.5 %random
Rwork0.234 ---
obs-16460 93.8 %-
Solvent computationBsol: 40.673 Å2
Displacement parametersBiso mean: 54.913 Å2
Baniso -1Baniso -2Baniso -3
1--2.926 Å2-15.293 Å20 Å2
2---2.926 Å20 Å2
3---5.853 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 5 0 4745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5781.5
X-RAY DIFFRACTIONc_scbond_it1.8152
X-RAY DIFFRACTIONc_mcangle_it2.8912
X-RAY DIFFRACTIONc_scangle_it3.1472.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param

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