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- PDB-3bce: Crystal structure of the ErbB4 kinase -

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Basic information

Entry
Database: PDB / ID: 3bce
TitleCrystal structure of the ErbB4 kinase
ComponentsReceptor tyrosine-protein kinase erbB-4
KeywordsTRANSFERASE / active conformation / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Receptor / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding ...establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding / PI3K events in ERBB4 signaling / mammary gland epithelial cell differentiation / embryonic pattern specification / positive regulation of protein localization to cell surface / neurotransmitter receptor localization to postsynaptic specialization membrane / neural crest cell migration / epidermal growth factor receptor activity / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / cell surface receptor signaling pathway via JAK-STAT / Long-term potentiation / PI3K events in ERBB2 signaling / SHC1 events in ERBB4 signaling / GABA-ergic synapse / mammary gland alveolus development / cell fate commitment / Nuclear signaling by ERBB4 / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cardiac muscle cell proliferation / regulation of cell migration / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / synapse assembly / cell surface receptor protein tyrosine kinase signaling pathway / Downregulation of ERBB4 signaling / lactation / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / basal plasma membrane / neurogenesis / postsynaptic density membrane / Signaling by ERBB2 TMD/JMD mutants / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / presynaptic membrane / nervous system development / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / postsynaptic membrane / protein tyrosine kinase activity / Estrogen-dependent gene expression / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / transcription cis-regulatory region binding / mitochondrial matrix / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / glutamatergic synapse / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
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
: / DI(HYDROXYETHYL)ETHER / Receptor tyrosine-protein kinase erbB-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsQiu, C.
CitationJournal: Structure / Year: 2008
Title: Mechanism of Activation and Inhibition of the HER4/ErbB4 Kinase.
Authors: Qiu, C. / Tarrant, M.K. / Choi, S.H. / Sathyamurthy, A. / Bose, R. / Banjade, S. / Pal, A. / Bornmann, W.G. / Lemmon, M.A. / Cole, P.A. / Leahy, D.J.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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-4
B: Receptor tyrosine-protein kinase erbB-4
C: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8306
Polymers112,4743
Non-polymers3553
Water3,891216
1
A: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5462
Polymers37,4911
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)37,4911
Polymers37,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7923
Polymers37,4911
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.723, 86.723, 120.008
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 678 - 965 / Label seq-ID: 2 - 289

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Receptor tyrosine-protein kinase erbB-4 / p180erbB4 / Tyrosine kinase-type cell surface receptor HER4


Mass: 37491.457 Da / Num. of mol.: 3 / Fragment: ErbB4 kinase domain (UNP residues 702-1029)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q15303, receptor protein-tyrosine kinase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 34855 / % possible obs: 100 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.107 / Χ2: 0.982 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.592.60.45734880.9151100
2.59-2.692.60.35334820.925199.9
2.69-2.822.60.31634480.9381100
2.82-2.962.60.23835240.9471100
2.96-3.152.60.18935031.0021100
3.15-3.392.60.11634330.9821100
3.39-3.732.60.08434801.0341100
3.73-4.272.60.06235021.0391100
4.27-5.382.60.05434981.0331100
5.38-302.60.04934971.0041100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 19.619 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.612 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1750 5 %RANDOM
Rwork0.195 ---
obs0.198 34814 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6865 0 21 216 7102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227031
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9749500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5985848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33423.833300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.553151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2821546
X-RAY DIFFRACTIONr_chiral_restr0.0940.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025167
X-RAY DIFFRACTIONr_nbd_refined0.2050.23180
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.218
X-RAY DIFFRACTIONr_mcbond_it0.4711.54385
X-RAY DIFFRACTIONr_mcangle_it0.76726927
X-RAY DIFFRACTIONr_scbond_it1.1233000
X-RAY DIFFRACTIONr_scangle_it1.8154.52573
Refine LS restraints NCS

Ens-ID: 1 / Number: 2259 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.430.5
2BMEDIUM POSITIONAL0.480.5
3CMEDIUM POSITIONAL0.370.5
1AMEDIUM THERMAL0.392
2BMEDIUM THERMAL0.382
3CMEDIUM THERMAL0.42
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 123 -
Rwork0.27 2438 -
all-2561 -
obs--99.88 %
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)
11.38710.8120.36877.5498-0.1182.4336-0.0844-0.2190.17290.02970.1080.1043-0.0058-0.0112-0.02360.1281-0.0379-0.04060.03470.0199-0.038712.41415.847230.1679
21.3068-0.1261.06350.8412-0.15583.6086-0.11860.0859-0.01590.04680.0257-0.0972-0.05660.32230.09290.0909-0.0657-0.00990.0670.00150.04927.015411.438216.0801
32.80780.01240.10991.48250.10493.4039-0.0162-0.0139-0.11390.01340.03460.0825-0.0067-0.0848-0.01840.0914-0.0527-0.02740.0428-0.01750.0155-6.40929.05574.5834
46.0449-2.179-0.25592.85750.44652.8880.0195-0.14930.13770.07590.0395-0.08620.0580.0243-0.0589-0.0060.03010.01460.00730.0344-0.08687.561633.077365.5748
50.9438-0.0323-0.27830.863-0.50683.6703-0.0017-0.1323-0.0875-0.07530.09220.0630.16730.0181-0.09060.03430.0249-0.0156-0.0304-0.00670.04967.785738.018950.5291
60.92580.0909-0.49823.57110.16731.92160.0068-0.06690.12460.00030.1021-0.0054-0.07780.0684-0.10890.02260.0273-0.0087-0.0186-0.00210.015411.392751.085240.3243
77.76952.3421.76051.76340.99992.48210.1746-0.0357-0.1380.0377-0.1321-0.1296-0.13730.0969-0.04250.0035-0.0316-0.0017-0.01360.0627-0.0648-36.584942.8094.6601
80.96030.28670.25971.5767-0.79553.361-0.05830.08680.02670.02860.08030.0146-0.14670.037-0.022-0.002-0.00250.0023-0.0247-0.00850.0348-36.075438.385215.3062
91.217-0.31430.0322.47040.12252.3542-0.04270.0161-0.0525-0.06350.0950.0452-0.05040.0613-0.05230.0132-0.04150.0095-0.03710.02050.0097-32.319224.044529.6079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA678 - 7372 - 61
2X-RAY DIFFRACTION2AA738 - 84662 - 170
3X-RAY DIFFRACTION3AA847 - 965171 - 289
4X-RAY DIFFRACTION4BB678 - 7502 - 74
5X-RAY DIFFRACTION5BB751 - 84675 - 170
6X-RAY DIFFRACTION6BB847 - 967171 - 291
7X-RAY DIFFRACTION7CC678 - 7082 - 32
8X-RAY DIFFRACTION8CC709 - 84633 - 170
9X-RAY DIFFRACTION9CC847 - 965171 - 289

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