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- PDB-4riy: Crystal structure of an EGFR/HER3 kinase domain heterodimer conta... -

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Basic information

Entry
Database: PDB / ID: 4riy
TitleCrystal structure of an EGFR/HER3 kinase domain heterodimer containing the cancer-associated HER3-E909G mutation
Components
  • Epidermal growth factor receptor
  • Receptor tyrosine-protein kinase erbB-3
KeywordsTRANSFERASE / RECEPTOR TYROSINE KINASE / PSEUDOKINASE / KINASE / ATP BINDING / MEMBRANE
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / negative regulation of cell adhesion / ErbB-3 class receptor binding / negative regulation of motor neuron apoptotic process / positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / motor neuron apoptotic process / 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 / regulation of peptidyl-tyrosine phosphorylation / response to UV-A / tongue development / PLCG1 events in ERBB2 signaling / midgut development / ERBB2-EGFR signaling pathway / digestive tract morphogenesis / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / ERBB2-ERBB3 signaling pathway / intracellular vesicle / growth factor binding / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / 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 / GAB1 signalosome / lateral plasma membrane / positive regulation of bone resorption / embryonic placenta development / negative regulation of signal transduction / Schwann cell development / positive regulation of phosphorylation / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of peptidyl-serine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / positive regulation of synaptic transmission, glutamatergic / Downregulation of ERBB2:ERBB3 signaling / ossification / positive regulation of DNA repair / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of epithelial cell proliferation / liver regeneration / epithelial cell proliferation / basal plasma membrane / Signal transduction by L1 / positive regulation of DNA replication / positive regulation of protein localization to plasma membrane / astrocyte activation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation
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 / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Epidermal growth factor receptor / Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.981 Å
AuthorsLittlefield, P. / Liu, L. / Jura, N.
CitationJournal: Sci.Signal. / Year: 2014
Title: Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations.
Authors: Littlefield, P. / Liu, L. / Mysore, V. / Shan, Y. / Shaw, D.E. / Jura, N.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Sep 20, 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_conn_angle / struct_conn / struct_ncs_dom_lim / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-3
B: Epidermal growth factor receptor
C: Receptor tyrosine-protein kinase erbB-3
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,13512
Polymers151,1714
Non-polymers1,9648
Water00
1
A: Receptor tyrosine-protein kinase erbB-3
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5676
Polymers75,5852
Non-polymers9824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-45 kcal/mol
Surface area25490 Å2
MethodPISA
2
C: Receptor tyrosine-protein kinase erbB-3
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5676
Polymers75,5852
Non-polymers9824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-47 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.334, 155.140, 87.297
Angle α, β, γ (deg.)90.00, 110.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSchain AAA680 - 9605 - 285
21VALVALLYSLYSchain CCC680 - 9605 - 285
12LEULEUASPASPchain BBB664 - 96011 - 307
22LEULEUASPASPchain DDD664 - 96011 - 307

NCS ensembles :
ID
1
2

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Components

#1: Protein Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 36418.086 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, UNP residues 698-1020 / Mutation: E909G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21860, receptor protein-tyrosine kinase
#2: Protein Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 39167.219 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, UNP residues 682-1022 / Mutation: V924R, F973A, L977A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00533, receptor protein-tyrosine kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.75 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/mL protein, 0.1M HEPES pH 7.5, 15% PEG-5000 MME, 5mM magnesium chloride, 0.5M ammonium acetate, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115867 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2014
RadiationMonochromator: KHOZU DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115867 Å / Relative weight: 1
ReflectionResolution: 2.981→60 Å / Num. all: 32503 / Num. obs: 32340 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GS6 AND 3KEX

2gs6

3kex


Resolution: 2.981→56.2 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 3251 10.05 %
Rwork0.2161 --
obs0.2212 32340 97.64 %
all-32503 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.981→56.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9002 0 120 0 9122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059334
X-RAY DIFFRACTIONf_angle_d1.09312673
X-RAY DIFFRACTIONf_dihedral_angle_d15.483496
X-RAY DIFFRACTIONf_chiral_restr0.0431428
X-RAY DIFFRACTIONf_plane_restr0.0061570
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2382X-RAY DIFFRACTION6.594TORSIONAL
12C2382X-RAY DIFFRACTION6.594TORSIONAL
21B2730X-RAY DIFFRACTION6.594TORSIONAL
22D2730X-RAY DIFFRACTION6.594TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9812-3.02570.3572920.3045737X-RAY DIFFRACTION59
3.0257-3.07290.33081610.29461314X-RAY DIFFRACTION100
3.0729-3.12330.35361290.26631301X-RAY DIFFRACTION100
3.1233-3.17720.37431300.27241279X-RAY DIFFRACTION100
3.1772-3.23490.29761470.26511298X-RAY DIFFRACTION100
3.2349-3.29710.31331550.26721279X-RAY DIFFRACTION100
3.2971-3.36440.33231590.24941251X-RAY DIFFRACTION100
3.3644-3.43760.28571180.25861332X-RAY DIFFRACTION100
3.4376-3.51750.30441450.23461280X-RAY DIFFRACTION100
3.5175-3.60550.25361460.21091291X-RAY DIFFRACTION100
3.6055-3.70290.29361500.2141280X-RAY DIFFRACTION100
3.7029-3.81190.26421340.21741299X-RAY DIFFRACTION99
3.8119-3.93490.26521340.20581273X-RAY DIFFRACTION100
3.9349-4.07550.26021460.21298X-RAY DIFFRACTION99
4.0755-4.23860.28211240.20381318X-RAY DIFFRACTION100
4.2386-4.43140.21891410.191294X-RAY DIFFRACTION99
4.4314-4.6650.20611480.17971287X-RAY DIFFRACTION99
4.665-4.95710.2381580.1781268X-RAY DIFFRACTION99
4.9571-5.33960.31411440.20981277X-RAY DIFFRACTION99
5.3396-5.87640.26991330.21461304X-RAY DIFFRACTION99
5.8764-6.72550.2231570.20591267X-RAY DIFFRACTION98
6.7255-8.46880.20811360.19521283X-RAY DIFFRACTION98
8.4688-56.20970.22081640.1881279X-RAY DIFFRACTION98
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)
10.077-0.04880.13944.1027-1.30821.7053-0.0057-0.1078-0.11020.03090.04210.05620.0541-0.1802-0.02430.18540.0174-0.02340.29290.02120.189810.1659-47.635422.6819
21.3738-0.4971-0.33162.2094-1.01791.69990.390.06810.0915-0.07490.07690.0499-0.0838-0.15120.09540.09440.0116-0.04680.22440.01880.16339.6714-29.11799.9664
30.47140.45690.34364.0156-0.10693.18810.0781-0.10070.02130.0464-0.1618-0.04960.0257-0.1073-0.00230.28350.00060.00110.24880.00730.196112.9051-13.82668.9824
42.43960.2745-0.093.7063-0.69392.15690.07220.09640.1170.1010.03360.222-0.1922-0.1080.00240.3050.04660.02090.1906-0.01170.1561.30461.2442-8.5154
51.32611.1161-0.56683.1196-0.61331.5097-0.05860.15370.2709-0.54140.19790.1045-0.14290.14250.05320.17310.0229-0.05030.25070.0820.251237.820526.8986-51.354
61.4023-0.0759-0.68153.5483-0.15343.458-0.0290.0004-0.0057-0.06690.08120.07830.11130.06070.02940.07480.0287-0.02230.1576-0.01560.164435.39236.3644-43.4956
71.7864-0.01-1.29523.4071-0.06652.40150.08170.0633-0.1585-0.2299-0.16020.04370.0838-0.1640.01870.30630.00410.0090.2538-0.00780.289631.0902-10.6346-38.6954
83.17980.26890.07883.7454-0.72792.6-0.01590.14640.1136-0.10020.04030.06530.0911-0.2058-0.00140.15310.01750.04760.1804-0.00880.188511.2834-25.6788-33.3971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 680:899)
2X-RAY DIFFRACTION2(chain A and resid 900:960)
3X-RAY DIFFRACTION3(chain B and resid 664:768)
4X-RAY DIFFRACTION4(chain B and resid 769:960)
5X-RAY DIFFRACTION5(chain C and resid 680:847)
6X-RAY DIFFRACTION6(chain C and resid 848:960)
7X-RAY DIFFRACTION7(chain D and resid 664:766)
8X-RAY DIFFRACTION8(chain D and resid 767:960)

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