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Basic information

Entry
Database: PDB / ID: 3njp
TitleThe Extracellular and Transmembrane Domain Interfaces in Epidermal Growth Factor Receptor Signaling
Components
  • Epidermal growth factor receptor
  • Epidermal growth factor
KeywordsTRANSFERASE / receptor tyrosine kinase
Function / homology
Function and homology information


negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / positive regulation of epithelial tube formation / positive regulation of ubiquitin-dependent protein catabolic process ...negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / positive regulation of epithelial tube formation / positive regulation of ubiquitin-dependent protein catabolic process / 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 / regulation of receptor signaling pathway via JAK-STAT / 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 / NFE2L2 regulating tumorigenic genes / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of nitric-oxide synthase activity / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / morphogenesis of an epithelial fold / intracellular vesicle / branching morphogenesis of an epithelial tube / 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 / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / eyelid development in camera-type eye / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / positive regulation of receptor internalization / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / mammary gland alveolus development / positive regulation of bone resorption / positive regulation of DNA binding / GAB1 signalosome / positive regulation of nitric oxide mediated signal transduction / salivary gland morphogenesis / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / ERK1 and ERK2 cascade / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in EGFR signaling / 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 / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / neurogenesis / cellular response to dexamethasone stimulus / SHC1 events in ERBB2 signaling / ossification / positive regulation of synaptic transmission, glutamatergic / guanyl-nucleotide exchange factor activity / basal plasma membrane / regulation of ERK1 and ERK2 cascade / positive regulation of mitotic nuclear division / neuron projection morphogenesis / positive regulation of endothelial cell migration / positive regulation of superoxide anion generation / platelet alpha granule lumen / positive regulation of DNA replication / positive regulation of peptidyl-threonine phosphorylation / Signal transduction by L1
Similarity search - Function
Pro-epidermal growth factor / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Calcium-binding EGF domain ...Pro-epidermal growth factor / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Calcium-binding EGF domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Six-bladed beta-propeller, TolB-like / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Coagulation Factor Xa inhibitory site / Laminin / Laminin / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Furin-like repeat / Furin-like repeats / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / Pro-epidermal growth factor / Epidermal growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.304 Å
AuthorsLu, C. / Mi, L.-Z. / Grey, M.J. / Zhu, J. / Graef, E. / Yokoyama, S. / Springer, T.A.
CitationJournal: Mol.Cell.Biol. / Year: 2010
Title: Structural evidence for loose linkage between ligand binding and kinase activation in the epidermal growth factor receptor.
Authors: Lu, C. / Mi, L.Z. / Grey, M.J. / Zhu, J. / Graef, E. / Yokoyama, S. / Springer, T.A.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Epidermal growth factor
D: Epidermal growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,81221
Polymers147,0864
Non-polymers4,72717
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-4 kcal/mol
Surface area66290 Å2
MethodPISA
2
A: Epidermal growth factor receptor
C: Epidermal growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,31210
Polymers73,5432
Non-polymers1,7708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint11 kcal/mol
Surface area34380 Å2
MethodPISA
3
B: Epidermal growth factor receptor
D: Epidermal growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,50011
Polymers73,5432
Non-polymers2,9579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-2 kcal/mol
Surface area35150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.167, 220.167, 113.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 67987.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Plasmid: pcDNA3.1/Zeo(+) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec8
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Protein/peptide Epidermal growth factor /


Mass: 5555.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGF / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6QBS2, UniProt: P01133*PLUS
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 5.38 Å3/Da / Density % sol: 77.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 15% PEG4000, 1% PEG6000, 75 mM Tris-HCl, 75 mM soidum acetate, and 200 mM NaCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 46667 / % possible obs: 98.2 % / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.078 / Χ2: 1.358 / Net I/av σ(I): 21.454 / Net I/σ(I): 11.6 / Num. measured all: 320883
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
3.3-3.420.35843450.94692.6
3.42-3.550.30645861.05597.6
3.55-3.720.25446441.15198.4
3.72-3.910.19546341.22798.1
3.91-4.160.14346451.30198.6
4.16-4.480.10946951.4398.9
4.48-4.930.0947071.49499.2
4.93-5.640.08747201.53199.4
5.64-7.10.07447871.54199.8
7.1-500.05149041.29799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IVO

1ivo


Resolution: 3.304→49.493 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: -0 / σ(F): 1.38 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2979 2320 4.97 %
Rwork0.2632 --
obs0.2649 45560 98.15 %
all-45560 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.304→49.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10222 0 308 24 10554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210814
X-RAY DIFFRACTIONf_angle_d0.54114513
X-RAY DIFFRACTIONf_dihedral_angle_d13.6564082
X-RAY DIFFRACTIONf_chiral_restr0.0371584
X-RAY DIFFRACTIONf_plane_restr0.0021882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3035-3.37090.37111370.3382384X-RAY DIFFRACTION91
3.3709-3.44420.32251290.30042473X-RAY DIFFRACTION94
3.4442-3.52430.32771340.26542586X-RAY DIFFRACTION98
3.5243-3.61240.27081350.24432596X-RAY DIFFRACTION99
3.6124-3.71010.26121430.23322570X-RAY DIFFRACTION98
3.7101-3.81920.28361380.23262572X-RAY DIFFRACTION98
3.8192-3.94240.26431250.22452616X-RAY DIFFRACTION98
3.9424-4.08330.27041220.2152598X-RAY DIFFRACTION99
4.0833-4.24670.27521200.22422626X-RAY DIFFRACTION99
4.2467-4.43980.25631360.22312635X-RAY DIFFRACTION99
4.4398-4.67370.24171740.20762589X-RAY DIFFRACTION99
4.6737-4.96630.28341230.21442634X-RAY DIFFRACTION99
4.9663-5.34940.25091540.21782644X-RAY DIFFRACTION99
5.3494-5.88690.28171460.22642647X-RAY DIFFRACTION100
5.8869-6.73690.25221330.23982677X-RAY DIFFRACTION100
6.7369-8.48090.27481380.25362703X-RAY DIFFRACTION100
8.4809-49.49880.35161330.32962773X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35711.32530.33131.41240.30370.7168-0.12950.23770.2021-0.2189-0.16740.2259-0.07090.1689-00.84510.00520.07790.65880.19740.7711107.462367.236945.4033
23.84-0.00570.51860.28130.11590.83960.0772-0.0129-0.2282-0.10320.05290.1956-0.18910.12830.00010.49360.0735-0.05660.5027-0.10840.988659.08147.057554.4143
30.1087-0.21640.0060.09650.2451-0.1090.18790.0981-0.8777-0.1693-0.7666-0.01160.6963-1.151702.10290.0533-0.15331.00880.17861.6316119.317713.995541.9995
40.08450.054-0.02330.11060.2631-0.1522-0.09260.54570.0582-0.4340.0475-0.3733-0.1630.65170.00011.3569-0.12960.06982.40611.12222.792587.212511.603986.6712
5-0.0198-0.0399-0.00970.01260.0445-0.0112-0.5459-0.69880.0319-0.31860.4872-0.02160.6628-0.2927-0.00011.931-0.6355-0.25462.18340.25212.7036106.8706-6.696560.8578
6-0.00480.00220.06210.05030.01910.0225-0.937-1.1657-0.1404-0.09670.75090.2592-0.7135-0.23970.00011.2909-0.2336-0.21672.76280.482.903114.19550.486477.5046
70.07570.06670.43320.0766-0.0450.0537-0.1499-0.4849-0.54170.2751-0.1259-0.31530.01880.68440.00021.2201-0.1777-0.02811.11640.12250.7569124.6975.693351.3984
80.1354-0.07150.12110.185-0.33690.3709-0.2349-0.1039-1.3444-1.0535-0.11430.71750.5595-0.3134-0.01280.71790.163-0.35660.9105-0.22441.735143.50835.795948.8784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 2:500
2X-RAY DIFFRACTION2chain B and resid 1:500
3X-RAY DIFFRACTION3chain A and resid 501:573
4X-RAY DIFFRACTION4chain B and resid 501:573
5X-RAY DIFFRACTION5chain A and resid 574:614
6X-RAY DIFFRACTION6chain B and resid 574:614
7X-RAY DIFFRACTION7chain C
8X-RAY DIFFRACTION8chain D

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