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- PDB-3gop: Crystal structure of the EGF receptor juxtamembrane and kinase domains -

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Basic information

Entry
Database: PDB / ID: 3gop
TitleCrystal structure of the EGF receptor juxtamembrane and kinase domains
ComponentsEpidermal growth factor receptor
KeywordsTRANSFERASE / kinase / juxtamembrane / EGFR / Anti-oncogene / ATP-binding / Cell cycle / Cell membrane / Disease mutation / Disulfide bond / Glycoprotein / Isopeptide bond / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


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 / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...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 / 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 / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / positive regulation of nitric oxide mediated signal transduction / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / positive regulation of DNA repair / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / ossification / positive regulation of synaptic transmission, glutamatergic / neurogenesis / cellular response to dexamethasone stimulus / basal plasma membrane / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / Signal transduction by L1 / epithelial cell proliferation / cellular response to estradiol stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of epithelial cell proliferation / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / clathrin-coated endocytic vesicle membrane / lung development / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / ruffle membrane
Similarity search - Function
: / 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 ...: / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsChoi, S.H. / Alvarado, D. / Moravcevic, K. / Lemmon, M.A.
CitationJournal: Mol.Cell / Year: 2009
Title: The juxtamembrane region of the EGF receptor functions as an activation domain.
Authors: Red Brewer, M. / Choi, S.H. / Alvarado, D. / Moravcevic, K. / Pozzi, A. / Lemmon, M.A. / Carpenter, G.
History
DepositionMar 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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


Theoretical massNumber of molelcules
Total (without water)41,6671
Polymers41,6671
Non-polymers00
Water905
1
A: Epidermal growth factor receptor

A: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)83,3352
Polymers83,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/41
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.073, 62.073, 177.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 41667.266 Da / Num. of mol.: 1 / Fragment: sequence database residues 669-1018 / Mutation: K721M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 10% PEG3350, 0.1M KCl, 0.1M Tris pH8.5, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2008
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9127 / % possible obs: 98.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.103 / Χ2: 1.369
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.857.80.3064521.2961100
2.85-2.97.80.2874291.31100
2.9-2.967.70.2564681.343199.6
2.96-3.027.90.2284291.3711100
3.02-3.0880.24541.3911100
3.08-3.157.60.1884411.538199.3
3.15-3.2380.1674481.6271100
3.23-3.327.80.1514421.598199.8
3.32-3.427.80.1314561.687199.1
3.42-3.537.70.1254471.717199.8
3.53-3.657.30.1214601.968199.8
3.65-3.87.80.1254402.728199.1
3.8-3.977.60.0894600.891199.6
3.97-4.187.80.0834580.738198.5
4.18-4.447.70.0764570.919198.9
4.44-4.797.60.0724621.058199.4
4.79-5.277.70.074580.988198.1
5.27-6.037.60.0714650.943198.1
6.03-7.597.30.0634871.013197.2
7.59-506.40.0535141.332192.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.17 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å39.33 Å
Translation2.8 Å39.33 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GS7

2gs7


Resolution: 2.8→39.33 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.817 / SU B: 31.834 / SU ML: 0.278 / SU R Cruickshank DPI: 0.366 / SU Rfree: 0.41 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES :RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 902 10 %RANDOM
Rwork0.208 ---
obs0.213 9024 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.22 Å2 / Biso mean: 24.873 Å2 / Biso min: 2.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å2-0 Å2
2--0.57 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 0 5 2385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222444
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9763313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17723.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.915435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9351519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211800
X-RAY DIFFRACTIONr_mcbond_it0.7261.51500
X-RAY DIFFRACTIONr_mcangle_it1.422427
X-RAY DIFFRACTIONr_scbond_it2.0233944
X-RAY DIFFRACTIONr_scangle_it3.3444.5884
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 77 -
Rwork0.282 565 -
all-642 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: -8.9357 Å / Origin y: -22.1793 Å / Origin z: -36.5158 Å
111213212223313233
T0.1478 Å2-0.0259 Å2-0.0057 Å2-0.0388 Å20.0113 Å2--0.0808 Å2
L0.2729 °2-0.0736 °2-0.0482 °2-0.7453 °20.9577 °2--1.4145 °2
S-0.0543 Å °0.0918 Å °0.0322 Å °-0.091 Å °0.0019 Å °0.0637 Å °-0.2389 Å °0.0465 Å °0.0523 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A652 - 994
2X-RAY DIFFRACTION1A1 - 6

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