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- PDB-2ahx: Crystal structure of ErbB4/HER4 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 2ahx
TitleCrystal structure of ErbB4/HER4 extracellular domain
ComponentsReceptor tyrosine-protein kinase erbB-4
KeywordsCELL CYCLE / SIGNALING PROTEIN / x-ray crystallography / neuregulins / heparin-binding
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 / Downregulation of ERBB4 signaling / lactation / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / neurogenesis / basal plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / 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
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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe ...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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / 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 / 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
YTTRIUM (III) ION / Receptor tyrosine-protein kinase erbB-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsBouyain, S. / Longo, P.A. / Li, S. / Ferguson, K.M. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The extracellular region of ErbB4 adopts a tethered conformation in the absence of ligand
Authors: Bouyain, S. / Longo, P.A. / Li, S. / Ferguson, K.M. / Leahy, D.J.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-4
B: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,97822
Polymers138,0622
Non-polymers3,91620
Water2,486138
1
A: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,89710
Polymers69,0311
Non-polymers1,8669
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,08212
Polymers69,0311
Non-polymers2,05111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Receptor tyrosine-protein kinase erbB-4
hetero molecules

B: Receptor tyrosine-protein kinase erbB-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,16324
Polymers138,0622
Non-polymers4,10122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area5880 Å2
ΔGint-7 kcal/mol
Surface area63650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.960, 203.090, 261.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-3001-

YT3

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Components

#1: Protein Receptor tyrosine-protein kinase erbB-4 / E.C.2.7.1.112 / p180erbB4 / Tyrosine kinase-type cell surface receptor HER4


Mass: 69030.859 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Cell (production host): Hampster Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1 / References: UniProt: Q15303, EC: 2.7.1.112
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate, PEG 3350, Bis-Tris, Yttrium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2005
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.396→30 Å / Num. all: 80870 / Num. obs: 80517 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.096 / Χ2: 1.027
Reflection shellResolution: 2.396→2.49 Å / % possible obs: 99.6 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.00997 / Mean I/σ(I) obs: 1.94 / Num. measured obs: 7940 / Num. unique all: 7940 / Χ2: 1.055 / % possible all: 99.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.396→29.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.554 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3901 5 %RANDOM
Rwork0.235 ---
all0.237 80517 --
obs0.237 77606 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---2.77 Å20 Å2
3---2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.396→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9562 0 240 138 9940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02110076
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.97413701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.43831222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.044151706
X-RAY DIFFRACTIONr_chiral_restr0.1070.21498
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027633
X-RAY DIFFRACTIONr_nbd_refined0.2540.34273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.5775
X-RAY DIFFRACTIONr_metal_ion_refined0.6670.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.3104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.513
X-RAY DIFFRACTIONr_mcbond_it1.4511.56088
X-RAY DIFFRACTIONr_mcangle_it2.55429846
X-RAY DIFFRACTIONr_scbond_it4.3633988
X-RAY DIFFRACTIONr_scangle_it6.6674.53855
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.342 237
Rwork0.329 4690
all-4927
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)
13.8047-0.85020.19773.6017-0.44344.23480.15770.46510.3949-0.3885-0.15770.3005-0.5079-0.358300.35920.1578-0.06560.20310.10630.244316.46136.769146.7
20.74490.2887-0.10454.2313-0.79691.42760.01210.06920.1601-0.3290.00350.0543-0.325-0.1374-0.01550.17010.08160.05540.24210.01260.266312.292119.719163.497
32.91050.7192-0.39592.4605-0.66387.1569-0.30940.0472-0.2334-0.10.1284-0.12010.90060.50190.18090.47740.16630.14760.30860.0690.132534.8176.596137.811
42.3441-2.3404-0.96535.15450.56872.07880.067-0.08020.0882-0.1004-0.10740.00720.01670.14140.04040.08880.0210.00610.27810.07980.156927.10689.051177.158
54.0828-0.4481-0.08063.51590.77733.593-0.03270.10710.2401-0.20860.0466-0.4305-0.07170.5313-0.01390.15070.03920.00780.16070.10820.142486.02221.95159.82
62.0523-1.3956-0.96692.44221.00411.77980.0456-0.11670.4429-0.06380.0256-0.3351-0.20950.1242-0.07120.19160.03650.00010.25180.06990.305272.87132.761177.735
74.033-0.5497-0.69463.1366-0.32782.2078-0.01620.142-0.3312-0.104-0.0343-0.15870.11190.07950.05050.0359-0.00390.05450.07060.050.206675.09386.484163.605
81.95732.6501-1.68026.1724-3.63532.6919-0.18810.1342-0.171-0.3957-0.0305-0.46140.44610.04770.21860.11850.03640.07890.14040.01510.091448.72859.498183.191
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1622 - 163
21AC10011
31AD10021
42AA163 - 308164 - 309
52AE10031
63AA309 - 475310 - 476
73AF10041
83AG10051
93AH10061
103AI10071
114AA476 - 616477 - 617
124AJ10081
135BB1 - 1622 - 163
145BK10091
155BL10101
165BM10111
176BB163 - 308164 - 309
186BN10121
197BB309 - 475310 - 476
207BO10131
217BP10141
227BQ10151
238BB476 - 614477 - 615
248BR10161

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