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- PDB-4zjv: crystal structure of EGFR kinase domain in complex with Mitogen-i... -

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Basic information

Entry
Database: PDB / ID: 4zjv
Titlecrystal structure of EGFR kinase domain in complex with Mitogen-inducible gene 6 protein
Components
  • ERBB receptor feedback inhibitor 1
  • Epidermal growth factor receptor
KeywordsTRANSFERASE/INHIBITOR / Epidermal growth factor receptor (EGFR) / ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein(Mig6) / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / 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 / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / lung vasculature development / 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 / intracellular vesicle / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / Signaling by ERBB4 / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / protein insertion into membrane / 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 / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / GRB2 events in EGFR signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / 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 / positive regulation of synaptic transmission, glutamatergic / cholesterol metabolic process / GTPase activator activity / ossification / neuron projection morphogenesis / positive regulation of epithelial cell proliferation / liver development / basal plasma membrane / cholesterol homeostasis / positive regulation of superoxide anion generation / liver regeneration / epithelial cell proliferation / response to progesterone / Signal transduction by L1 / positive regulation of DNA replication / protein localization to plasma membrane / neurogenesis / positive regulation of protein localization to plasma membrane / astrocyte activation / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of smooth muscle cell proliferation / response to insulin
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 / Resolution: 2.7 Å
AuthorsEck, M.J. / Park, E. / Lee, B.
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
DepositionApr 29, 2015Deposition 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 1.3Sep 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)90,8804
Polymers90,8804
Non-polymers00
Water1,72996
1
A: Epidermal growth factor receptor
C: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)45,4402
Polymers45,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-25 kcal/mol
Surface area15610 Å2
MethodPISA
2
B: Epidermal growth factor receptor
D: ERBB receptor feedback inhibitor 1


Theoretical massNumber of molelcules
Total (without water)45,4402
Polymers45,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-25 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.459, 81.865, 96.190
Angle α, β, γ (deg.)90.00, 106.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37636.441 Da / Num. of mol.: 2 / Fragment: Kinase domain (UNP residues 695-1022)
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: 7803.705 Da / Num. of mol.: 2 / Fragment: UNP residues 330-399 / Mutation: S390C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERRFI1, MIG6 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJM3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris 0.2 M Ammonium acetate 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 23122 / % possible obs: 96.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RF9

2rf9


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.084 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23197 1099 5.1 %RANDOM
Rwork0.17854 ---
obs0.18125 20535 89.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.06 Å2
2---0.07 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5171 0 0 96 5267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195295
X-RAY DIFFRACTIONr_bond_other_d0.0010.025199
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9957182
X-RAY DIFFRACTIONr_angle_other_deg0.694312015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5325638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20823.842203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52115950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0051527
X-RAY DIFFRACTIONr_chiral_restr0.0640.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021111
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3914.282579
X-RAY DIFFRACTIONr_mcbond_other3.3814.2792578
X-RAY DIFFRACTIONr_mcangle_it5.3236.3973205
X-RAY DIFFRACTIONr_mcangle_other5.3236.43206
X-RAY DIFFRACTIONr_scbond_it3.9594.6752716
X-RAY DIFFRACTIONr_scbond_other3.9354.6722714
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.296.8353976
X-RAY DIFFRACTIONr_long_range_B_refined8.50433.3715840
X-RAY DIFFRACTIONr_long_range_B_other8.49133.3815820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 33 -
Rwork0.268 882 -
obs--51.55 %

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