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- PDB-4gfv: PTPN18 in complex with HER2-pY1196 phosphor-peptides -

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Basic information

Entry
Database: PDB / ID: 4gfv
TitlePTPN18 in complex with HER2-pY1196 phosphor-peptides
Components
  • HER2-pY1196 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 / Interleukin-37 signaling / blastocyst formation / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Downregulation of ERBB2 signaling / nucleoplasm / nucleus ...negative regulation of ERBB signaling pathway / Interleukin-37 signaling / blastocyst formation / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Downregulation of ERBB2 signaling / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 ...: / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 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 1.0Oct 23, 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

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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
B: Tyrosine-protein phosphatase non-receptor type 18
E: HER2-pY1196 phosphor-peptide
F: HER2-pY1196 phosphor-peptide


Theoretical massNumber of molelcules
Total (without water)69,0654
Polymers69,0654
Non-polymers00
Water2,144119
1
A: Tyrosine-protein phosphatase non-receptor type 18
F: HER2-pY1196 phosphor-peptide


Theoretical massNumber of molelcules
Total (without water)34,5322
Polymers34,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-9 kcal/mol
Surface area12000 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 18
E: HER2-pY1196 phosphor-peptide


Theoretical massNumber of molelcules
Total (without water)34,5322
Polymers34,5322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-10 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.348, 91.341, 92.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 26:43 or resseq 46:62 or resseq...
211chain B and (resseq 26:43 or resseq 46:62 or resseq...

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Components

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


Mass: 33733.562 Da / Num. of mol.: 2 / 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-pY1196 phosphor-peptide


Mass: 798.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
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: 2.095→80 Å / Num. obs: 36335 / % possible obs: 96.48 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 2.095→2.2786 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: 2.095→49.002 Å / SU ML: 0.35 / Isotropic thermal model: Overall / σ(F): 0 / Phase error: 32.62 / Stereochemistry target values: MLHL / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflection
Rfree0.293 1809 4.99 %
Rwork0.2459 --
obs0.2483 36238 95.59 %
all-36335 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.971 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.923 Å20 Å2-0 Å2
2--13.7246 Å20 Å2
3----2.8016 Å2
Refinement stepCycle: LAST / Resolution: 2.095→49.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 0 119 4797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014657
X-RAY DIFFRACTIONf_angle_d1.2776318
X-RAY DIFFRACTIONf_dihedral_angle_d15.3871697
X-RAY DIFFRACTIONf_chiral_restr0.074692
X-RAY DIFFRACTIONf_plane_restr0.005816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1971X-RAY DIFFRACTIONPOSITIONAL
12B1971X-RAY DIFFRACTIONPOSITIONAL0.072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.095-2.17010.44471650.39953180X-RAY DIFFRACTION89
2.1701-2.2570.38391650.34683267X-RAY DIFFRACTION92
2.257-2.35970.35861790.31383327X-RAY DIFFRACTION94
2.3597-2.48410.35641730.28423397X-RAY DIFFRACTION95
2.4841-2.63970.29491740.26623425X-RAY DIFFRACTION96
2.6397-2.84350.31511820.25973430X-RAY DIFFRACTION96
2.8435-3.12960.27711950.23563513X-RAY DIFFRACTION98
3.1296-3.58240.26351840.20793573X-RAY DIFFRACTION99
3.5824-4.51290.24952090.18913585X-RAY DIFFRACTION99
4.5129-49.01520.24191830.20953732X-RAY DIFFRACTION98

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