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- PDB-3lmg: Crystal structure of the ERBB3 kinase domain in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 3lmg
TitleCrystal structure of the ERBB3 kinase domain in complex with AMP-PNP
ComponentsReceptor tyrosine-protein kinase erbB-3
KeywordsTRANSFERASE / ERBB3 / HER3 / tyrosine kinase domain / AMP-PNP / Nucleotide binding
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 / motor neuron apoptotic process / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / growth factor binding / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / negative regulation of signal transduction / Schwann cell development / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / myelination / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / basal plasma membrane / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heart development / regulation of cell population proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / apical plasma membrane / protein heterodimerization activity / phosphorylation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsShi, F. / Lemmon, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation.
Authors: Shi, F. / Telesco, S.E. / Liu, Y. / Radhakrishnan, R. / Lemmon, M.A.
History
DepositionJan 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_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.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5286
Polymers77,4672
Non-polymers1,0614
Water1267
1
A: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2643
Polymers38,7341
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2643
Polymers38,7341
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.348, 47.981, 82.224
Angle α, β, γ (deg.)90.000, 108.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Receptor tyrosine-protein kinase erbB-3 / c-erbB3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 38733.570 Da / Num. of mol.: 2 / Fragment: Tyrosine Kinase Domain (UNP residues 684-1020)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21860, receptor protein-tyrosine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM MOPS pH7.4, 27% (w/v) PEG8000, 0.17 M ammonium sulfate and 15%(v/v) glycerol in well solution and 5mM MgCl2 and 1mM AMP-PNP in protein solution, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 17805 / Num. obs: 16021 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Χ2: 1.444 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.2 / Num. unique all: 484 / Rsym value: 0.499 / Χ2: 1.39 / % possible all: 55.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GS7

2gs7


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 38.69 / SU ML: 0.371 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.469 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1612 10.1 %RANDOM
Rwork0.252 ---
obs0.255 16018 89.14 %-
all-17805 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.55 Å2 / Biso mean: 30.947 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å21.19 Å2
2---1.87 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 64 7 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224382
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9845960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6845529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08323.559177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00915744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5991525
X-RAY DIFFRACTIONr_chiral_restr0.0680.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213211
X-RAY DIFFRACTIONr_mcbond_it0.2061.52663
X-RAY DIFFRACTIONr_mcangle_it0.38424299
X-RAY DIFFRACTIONr_scbond_it0.30731719
X-RAY DIFFRACTIONr_scangle_it0.5724.51661
LS refinement shellResolution: 2.804→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 57 -
Rwork0.333 589 -
all-646 -
obs--50.16 %
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)
13.41930.4637-0.01783.7402-2.83747.46210.02880.0471-0.1558-0.21250.09-0.21820.61910.1476-0.11890.08290.0636-0.07780.35130.0090.231723.433-35.58145.425
26.0648-1.0828-0.19342.49230.27773.8879-0.1148-0.77090.02610.57450.11110.5227-0.1631-0.64450.00380.27930.15970.11240.68030.08820.29267.033-30.68464.046
34.0734-0.29720.24452.8083-1.86847.0335-0.086-0.34180.09490.24220.0665-0.1892-0.47290.41870.01950.1003-0.062-0.12640.3819-0.01040.251923.346-14.64932.484
45.01630.05520.68563.93790.81085.91850.14510.3359-0.323-0.323-0.24650.3940.2448-0.47270.10150.1122-0.0377-0.13990.4108-0.03520.2247.214-19.82614.276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A680 - 774
2X-RAY DIFFRACTION2A775 - 959
3X-RAY DIFFRACTION3B680 - 774
4X-RAY DIFFRACTION4B775 - 959

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