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- PDB-4gfu: PTPN18 in complex with HER2-pY1248 phosphor-peptides -

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Basic information

Entry
Database: PDB / ID: 4gfu
TitlePTPN18 in complex with HER2-pY1248 phosphor-peptides
Components
  • HER2-pY1248 phosphor-peptide
  • Tyrosine-protein phosphatase non-receptor type 18
KeywordsHYDROLASE/Peptide / phosphatase / tyrosine phosphorylation / hydrolase / HYDROLASE-Peptide complex
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding ...negative regulation of ERBB signaling pathway / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / blastocyst formation / Interleukin-37 signaling / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / ERBB2 Activates PTK6 Signaling / enzyme-linked receptor protein signaling pathway / neuromuscular junction development / ERBB2-ERBB3 signaling pathway / positive regulation of Rho protein signal transduction / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / positive regulation of transcription by RNA polymerase I / positive regulation of MAP kinase activity / ERBB2 Regulates Cell Motility / non-membrane spanning protein tyrosine phosphatase activity / semaphorin-plexin signaling pathway / oligodendrocyte differentiation / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / protein dephosphorylation / Downregulation of ERBB2:ERBB3 signaling / coreceptor activity / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / transmembrane receptor protein tyrosine kinase activity / protein-tyrosine-phosphatase / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / protein tyrosine phosphatase activity / basal plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / cellular response to epidermal growth factor stimulus / peptidyl-tyrosine phosphorylation / positive regulation of translation / positive regulation of epithelial cell proliferation / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / Downregulation of ERBB2 signaling / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / cellular response to growth factor stimulus / ruffle membrane / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / early endosome / cell surface receptor signaling pathway / endosome membrane / cell population proliferation / protein phosphorylation / receptor complex / positive regulation of MAPK cascade / intracellular signal transduction / apical plasma membrane / protein heterodimerization activity / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction
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 / Protein tyrosine phosphatase superfamily / Receptor L-domain / Furin-like cysteine-rich 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 / Protein tyrosine phosphatase superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Protein-Tyrosine Phosphatase; Chain A / Furin-like repeat / Furin-like repeats / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2 / Tyrosine-protein phosphatase non-receptor type 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H.M. / Yang, F. / Du, Y.J. / Yang, D.X. / Zhang, Y. / Yu, X. / Sun, J.P.
CitationJournal: To be Published
Title: PTPN18-HER2 peptides
Authors: Wang, H.M. / Yang, F. / Du, Y.J. / Yang, D.X. / Zhang, Y. / Yu, X. / Sun, J.P.
History
DepositionAug 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 18
F: HER2-pY1248 phosphor-peptide


Theoretical massNumber of molelcules
Total (without water)34,6192
Polymers34,6192
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-10 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.032, 71.766, 57.161
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 18 / Brain-derived phosphatase


Mass: 33733.562 Da / Num. of mol.: 1 / Fragment: UNP residues 6-300 / Mutation: C229S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN18, BDP1 / Plasmid: PGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99952, protein-tyrosine-phosphatase
#2: Protein/peptide HER2-pY1248 phosphor-peptide


Mass: 885.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04626*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 18%-22% PEG4K, 6% Jeffamine M 600, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.98
SYNCHROTRONBSRF 3W1A21
Detector
TypeIDDetectorDate
SYNTEX1DIFFRACTOMETERAug 7, 2011
SYNTEX2DIFFRACTOMETERJun 5, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
211
ReflectionResolution: 2→80 Å / Num. all: 23873 / Num. obs: 22674 / % possible obs: 95.33 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2→2.091 Å / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OC3

2oc3


Resolution: 2→33.26 Å / SU ML: 0.21 / Isotropic thermal model: Overall / σ(F): 0 / Phase error: 23.34 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflection
Rfree0.2319 1154 5.09 %
Rwork0.1894 --
obs0.1915 22674 95.33 %
all-23873 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.615 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.0222 Å2-0 Å26.8767 Å2
2--3.8613 Å2-0 Å2
3---9.1609 Å2
Refinement stepCycle: LAST / Resolution: 2→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 0 146 2338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062242
X-RAY DIFFRACTIONf_angle_d1.0163037
X-RAY DIFFRACTIONf_dihedral_angle_d13.689832
X-RAY DIFFRACTIONf_chiral_restr0.065332
X-RAY DIFFRACTIONf_plane_restr0.004388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.29781290.23152489X-RAY DIFFRACTION89
2.091-2.20120.22251340.20452602X-RAY DIFFRACTION93
2.2012-2.33910.23891440.19012615X-RAY DIFFRACTION93
2.3391-2.51970.25591360.1992666X-RAY DIFFRACTION95
2.5197-2.77310.26981620.19622714X-RAY DIFFRACTION96
2.7731-3.17410.24621540.2012758X-RAY DIFFRACTION98
3.1741-3.9980.1971410.16322816X-RAY DIFFRACTION99
3.998-33.2650.221540.18862860X-RAY DIFFRACTION99

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