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- PDB-3d44: Crystal structure of HePTP in complex with a dually phosphorylate... -

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Basic information

Entry
Database: PDB / ID: 3d44
TitleCrystal structure of HePTP in complex with a dually phosphorylated Erk2 peptide mimetic
Components
  • Mitogen-activated protein kinase 1 peptide
  • Tyrosine-protein phosphatase non-receptor type 7
KeywordsHYDROLASE / HEPTP / HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT / LC-PTP / PTPN7 / ERK2 / PTP-PEPTIDE COMPLEX / MAPK-DERIVED PEPTIDE / Phosphoprotein / Protein phosphatase
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / Signaling by MAP2K mutants ...phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / Signaling by MAP2K mutants / Signaling by NODAL / ERKs are inactivated / response to epidermal growth factor / RSK activation / Interleukin-37 signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / labyrinthine layer blood vessel development / ERBB signaling pathway / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / positive regulation of peptidyl-threonine phosphorylation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / MAPK1 (ERK2) activation / positive regulation of macrophage chemotaxis / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / face development / lung morphogenesis / positive regulation of telomere maintenance / Recycling pathway of L1 / pseudopodium / Bergmann glial cell differentiation / androgen receptor signaling pathway / thyroid gland development / steroid hormone receptor signaling pathway / Advanced glycosylation endproduct receptor signaling / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / negative regulation of cell differentiation / regulation of ossification / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate WASPs and WAVEs / JUN kinase activity / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / phosphatase binding / Schwann cell development / Growth hormone receptor signaling / progesterone receptor signaling pathway / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / protein dephosphorylation / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / myelination / protein tyrosine phosphatase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / protein-tyrosine-phosphatase / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / ERK1 and ERK2 cascade / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ESR-mediated signaling / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to nicotine / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / positive regulation of cholesterol biosynthetic process / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling
Similarity search - Function
Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase 1 / Tyrosine-protein phosphatase non-receptor type 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCritton, D.A. / Tortajada, A. / Page, R.
CitationJournal: Biochemistry / Year: 2008
Title: Structural basis of substrate recognition by hematopoietic tyrosine phosphatase.
Authors: Critton, D.A. / Tortajada, A. / Stetson, G. / Peti, W. / Page, R.
History
DepositionMay 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 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 7
B: Mitogen-activated protein kinase 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4486
Polymers36,2502
Non-polymers1984
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-34.4 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.072, 38.880, 83.698
Angle α, β, γ (deg.)90.00, 124.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 7 / Protein-tyrosine phosphatase LC-PTP / Hematopoietic protein-tyrosine phosphatase / HEPTP


Mass: 35202.711 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 65-360) / Mutation: T106D, C270S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P35236, protein-tyrosine-phosphatase
#2: Protein/peptide Mitogen-activated protein kinase 1 peptide / Extracellular signal-regulated kinase 2 / ERK-2 / Mitogen-activated protein kinase 2 / MAP kinase 2 ...Extracellular signal-regulated kinase 2 / ERK-2 / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2 / p42-MAPK / ERT1


Mass: 1047.034 Da / Num. of mol.: 1 / Fragment: Activation loop (UNP residues 184-191) / Mutation: T183D / Source method: obtained synthetically
Details: THIS SEQUENCE RESEMBLES THAT WHICH OCCURS NATURALLY IN HUMANS
References: UniProt: P28482
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.0 M LITHIUM CHLORIDE, 0.1 M CITRATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 28, 2008
Details: SI(III) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(III) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 25161 / Num. obs: 24617 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.102
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.459 / Num. unique all: 2479 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d42

3d42


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.752 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20426 1283 5.1 %RANDOM
Rwork0.16352 ---
all0.174 24572 --
obs0.16565 23842 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.895 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20.52 Å2
2---0.13 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 9 271 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222360
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9613210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4623.772114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8591518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021820
X-RAY DIFFRACTIONr_nbd_refined0.1940.21131
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21584
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.223
X-RAY DIFFRACTIONr_mcbond_it1.69831490
X-RAY DIFFRACTIONr_mcangle_it2.69252337
X-RAY DIFFRACTIONr_scbond_it4.36981001
X-RAY DIFFRACTIONr_scangle_it6.31811873
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 92 -
Rwork0.197 1721 -
obs--99.51 %

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