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- PDB-4riw: Crystal structure of an EGFR/HER3 kinase domain heterodimer -

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Basic information

Entry
Database: PDB / ID: 4riw
TitleCrystal structure of an EGFR/HER3 kinase domain heterodimer
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 / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic 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 / motor neuron apoptotic process / 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 / ERBB2-ERBB3 signaling pathway / 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 / growth factor binding / 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 / lateral plasma membrane / 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 / Schwann cell development / negative regulation of 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 / extrinsic apoptotic signaling pathway in absence of ligand / 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 / myelination / Downregulation of ERBB2:ERBB3 signaling / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of DNA replication / Signal transduction by L1
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
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: 3.1 Å
AuthorsLittlefield, P. / 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)153,27912
Polymers151,3154
Non-polymers1,9648
Water0
1
A: Receptor tyrosine-protein kinase erbB-3
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6396
Polymers75,6572
Non-polymers9824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-41 kcal/mol
Surface area25080 Å2
MethodPISA
2
C: Receptor tyrosine-protein kinase erbB-3
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6396
Polymers75,6572
Non-polymers9824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-43 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.780, 154.640, 86.970
Angle α, β, γ (deg.)90.00, 110.89, 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: 36490.148 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, UNP residues 698-1020
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, ERBB, ERBB1, HER1 / 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 / Adenosine 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7 mg/mL protein, 0.1M HEPES pH 7.5, 14% PEG-6000, 0.2M magnesium chloride, 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: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2014
RadiationMonochromator: KHOZU DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 3.1→60.48 Å / Num. all: 29435 / Num. obs: 28729 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 5.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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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: 3.1→60.476 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 29.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 2864 9.97 %
Rwork0.2267 --
obs0.2327 28729 97.42 %
all-29435 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→60.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9023 0 120 0 9143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059355
X-RAY DIFFRACTIONf_angle_d0.98212701
X-RAY DIFFRACTIONf_dihedral_angle_d14.9033510
X-RAY DIFFRACTIONf_chiral_restr0.0391430
X-RAY DIFFRACTIONf_plane_restr0.0051575
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2346X-RAY DIFFRACTION8.413TORSIONAL
12C2346X-RAY DIFFRACTION8.413TORSIONAL
21B2642X-RAY DIFFRACTION8.413TORSIONAL
22D2642X-RAY DIFFRACTION8.413TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.15350.38971300.32611347X-RAY DIFFRACTION99
3.1535-3.21080.38031590.30411254X-RAY DIFFRACTION99
3.2108-3.27260.41711370.29861359X-RAY DIFFRACTION99
3.2726-3.33940.35811410.28651301X-RAY DIFFRACTION99
3.3394-3.4120.36771410.27141318X-RAY DIFFRACTION99
3.412-3.49130.30671670.26071307X-RAY DIFFRACTION99
3.4913-3.57860.30951350.24061279X-RAY DIFFRACTION99
3.5786-3.67540.33321570.22881332X-RAY DIFFRACTION99
3.6754-3.78350.25781400.23611291X-RAY DIFFRACTION98
3.7835-3.90560.26611270.22161321X-RAY DIFFRACTION99
3.9056-4.04520.29821510.21431292X-RAY DIFFRACTION98
4.0452-4.20710.28011510.19911287X-RAY DIFFRACTION98
4.2071-4.39850.23531330.19911324X-RAY DIFFRACTION97
4.3985-4.63030.24161450.19051272X-RAY DIFFRACTION97
4.6303-4.92030.24471460.19311300X-RAY DIFFRACTION97
4.9203-5.30.26791280.20191268X-RAY DIFFRACTION96
5.3-5.8330.31641520.22071264X-RAY DIFFRACTION95
5.833-6.67610.26351420.21451262X-RAY DIFFRACTION94
6.6761-8.40760.22541510.20211230X-RAY DIFFRACTION93
8.4076-60.48740.22321310.19341257X-RAY DIFFRACTION92
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)
10.57290.1448-0.08532.0616-0.67922.273-0.001-0.0949-0.2145-0.1047-0.00220.04490.4866-0.1208-0.04780.08270.0015-0.01960.22270.00760.180310.2635-47.546222.7701
21.2323-0.2859-0.57661.0552-0.26791.02250.1231-0.09030.0237-0.0354-0.06810.00650.1303-0.1970.12360.1861-0.0368-0.12240.1840.01690.10049.7392-28.857810.3315
31.0743-0.06540.13213.21180.75852.48610.1226-0.151-0.1909-0.0686-0.1406-0.0375-0.045-0.2611-0.02760.190.0054-0.03240.1317-0.02660.166412.7581-14.06888.7481
42.69640.21680.09982.4912-0.52941.39850.1920.04470.03660.0277-0.03670.2806-0.1486-0.15080.01850.34020.01870.07890.1808-0.00420.13081.23230.9989-8.5902
50.80791.328-0.73633.7699-0.41461.87190.08080.11750.2444-0.20150.04360.2227-0.13470.04060.00750.19890.03380.01980.19390.0330.218537.699326.8661-51.3654
60.92040.83780.14721.5475-0.43532.16440.0022-0.03220.02610.1004-0.0005-0.13030.08570.03110.07150.0272-0.00330.01080.1685-0.06880.213735.41886.3068-43.5481
71.43410.0261-1.31413.29140.07312.43720.04980.24360.01410.0226-0.10580.1168-0.116-0.15990.08690.11190.00330.0280.2058-0.01260.130131.007-10.4048-38.712
82.61080.4280.45722.3958-0.27231.7615-0.06330.08250.0366-0.1526-0.01090.020.1162-0.0635-0.01720.08090.0023-0.01060.1264-0.01340.128611.1737-25.4018-33.3829
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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