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- PDB-2gph: Docking motif interactions in the MAP kinase ERK2 -

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Basic information

Entry
Database: PDB / ID: 2gph
TitleDocking motif interactions in the MAP kinase ERK2
Components
  • Mitogen-activated protein kinase 1
  • Tyrosine-protein phosphatase non-receptor type 7
KeywordsTRANSFERASE / ERK2 / docking interaction / D-motif / allostery / CD-site / phosphatase-derived peptide / processing conformation
Function / homology
Function and homology information


phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / IFNG signaling activates MAPKs / Golgi Cisternae Pericentriolar Stack Reorganization / RHO GTPases Activate WASPs and WAVEs / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / Oxidative Stress Induced Senescence / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signaling by Activin / Negative regulation of FGFR2 signaling / Signal transduction by L1 / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / diadenosine tetraphosphate biosynthetic process / MAP2K and MAPK activation / neural crest cell development / Recycling pathway of L1 / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / cellular response to methionine / cellular response to toxic substance / Interleukin-37 signaling / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / regulation of Golgi inheritance / RAF/MAP kinase cascade / mitogen-activated protein kinase kinase kinase binding / response to alcohol / ERBB signaling pathway / Thrombin signalling through proteinase activated receptors (PARs) / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / steroid hormone receptor signaling pathway / cellular response to insulin-like growth factor stimulus / androgen receptor signaling pathway / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / response to testosterone / regulation of cytoskeleton organization / response to exogenous dsRNA / pseudopodium / lung morphogenesis / face development / positive regulation of telomere maintenance / Bergmann glial cell differentiation / decidualization / non-membrane spanning protein tyrosine phosphatase activity / thyroid gland development / peptidyl-threonine phosphorylation / progesterone receptor signaling pathway / regulation of ossification / MAP kinase activity / negative regulation of cell differentiation / mitogen-activated protein kinase / phosphatase binding / estrous cycle / Schwann cell development / protein dephosphorylation / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / cellular response to platelet-derived growth factor stimulus / ERK1 and ERK2 cascade / phosphotyrosine residue binding / myelination / sensory perception of pain / protein-tyrosine-phosphatase / RNA polymerase II CTD heptapeptide repeat kinase activity
Similarity search - Function
Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein (MAP) kinase, ERK1/2 / 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, KIM-containing / Mitogen-activated protein (MAP) kinase, ERK1/2 / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 7 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhou, T. / Sun, L. / Humphreys, J. / Goldsmith, E.J.
CitationJournal: Structure / Year: 2006
Title: Docking Interactions Induce Exposure of Activation Loop in the MAP Kinase ERK2.
Authors: Zhou, T. / Sun, L. / Humphreys, J. / Goldsmith, E.J.
History
DepositionApr 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
B: Tyrosine-protein phosphatase non-receptor type 7


Theoretical massNumber of molelcules
Total (without water)44,0262
Polymers44,0262
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.981, 66.342, 116.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 1 / 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: 42161.473 Da / Num. of mol.: 1 / Mutation: C115T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erk2 / Production host: Escherichia coli (E. coli)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Protein/peptide Tyrosine-protein phosphatase non-receptor type 7 / Protein-tyrosine phosphatase LC-PTP / Hematopoietic protein-tyrosine phosphatase / HEPTP


Mass: 1864.180 Da / Num. of mol.: 1 / Mutation: C52V / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P35236, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 10% isopropanol, 0.1M sodium HEPES, pH 7.5, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97112 Å
DetectorDate: Jan 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97112 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29041

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Phasing

Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.56-500.0137.0940.951198
4.41-5.5637.8260.9391192
3.85-4.4130.1890.961148
3.5-3.8536.9080.931171
3.25-3.526.6410.941170
3.06-3.2528.9780.91124
2.9-3.0623.1690.8971127
2.78-2.921.9510.8781119
2.67-2.7815.8750.9271106
2.58-2.6716.3270.8951080
2.5-2.5814.6280.9071124
2.43-2.513.4740.931044
2.36-2.4314.490.8661075
2.31-2.3613.8140.8681042
2.25-2.3114.3050.8971006
2.2-2.2515.0940.8391010
2.16-2.211.20.8781045
2.12-2.1610.4380.891011
2.08-2.1210.0750.889994
2.05-2.0811.9410.841966
2.01-2.0512.5870.842893
1.98-2.019.3890.835829
1.95-1.9810.5290.803796
1.93-1.959.6610.764656
1.9-1.9313.3730.702640

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1ERK

1erk
PDB Unreleased entry


Resolution: 1.9→50 Å / FOM work R set: 0.807 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 1270 4.4 %
Rwork0.216 --
all0.231 --
obs0.231 25566 88.9 %
Solvent computationBsol: 52.789 Å2
Displacement parametersBiso mean: 36.818 Å2
Baniso -1Baniso -2Baniso -3
1-2.357 Å20 Å20 Å2
2--5.586 Å20 Å2
3----7.944 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 290 3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5461.5
X-RAY DIFFRACTIONc_scbond_it2.3082
X-RAY DIFFRACTIONc_mcangle_it2.4212
X-RAY DIFFRACTIONc_scangle_it3.3732.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.930.338390.414601640
1.93-1.950.432360.365620656
1.95-1.980.394460.328750796
1.98-2.010.306390.323790829
2.01-2.050.345460.302847893
2.05-2.080.29330.296933966
2.08-2.120.261430.258951994
2.12-2.160.289490.2539621011
2.16-2.20.272560.2369891045
2.2-2.250.335460.2939641010
2.25-2.310.258400.2569661006
2.31-2.360.303560.2199861042
2.36-2.430.313490.2210261075
2.43-2.50.207580.1969861044
2.5-2.580.261690.2210551124
2.58-2.670.299510.20310291080
2.67-2.780.223540.19610521106
2.78-2.90.312730.23510461119
2.9-3.060.301460.22610811127
3.06-3.250.299570.21210671124
3.25-3.50.228540.19111161170
3.5-3.850.255490.19911221171
3.85-4.410.203590.15810891148
4.41-5.560.23660.1911261192
5.56-500.010.253560.21211421198
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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