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- PDB-9c66: Structure of the Mena EVH1 domain bound to the polyproline segmen... -

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Basic information

Entry
Database: PDB / ID: 9c66
TitleStructure of the Mena EVH1 domain bound to the polyproline segment of PTP1B
Components
  • Protein enabled homolog
  • poly-proline segment of PTP1B
KeywordsSTRUCTURAL PROTEIN / Mena
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / WW domain binding / positive regulation of receptor catabolic process / insulin receptor recycling ...postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / WW domain binding / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of vascular associated smooth muscle cell migration / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / regulation of proteolysis / Generation of second messenger molecules / positive regulation of JUN kinase activity / cellular response to fibroblast growth factor stimulus / growth hormone receptor signaling pathway via JAK-STAT / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / positive regulation of cardiac muscle cell apoptotic process / MECP2 regulates neuronal receptors and channels / protein dephosphorylation / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Integrin signaling / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axon guidance / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / GABA-ergic synapse / filopodium / insulin receptor binding / cellular response to nerve growth factor stimulus / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / receptor tyrosine kinase binding / SH3 domain binding / insulin receptor signaling pathway / lamellipodium / negative regulation of neuron projection development / actin binding / actin cytoskeleton organization / cellular response to hypoxia / cytoskeleton / early endosome / postsynapse / mitochondrial matrix / cadherin binding / negative regulation of cell population proliferation / focal adhesion / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase, catalytic domain ...VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 / PH-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 1 / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLaComb, L. / Fedorov, E. / Bonanno, J.B. / Almo, S.C. / Ghosh, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biochemistry / Year: 2024
Title: Insights into the Interaction Landscape of the EVH1 Domain of Mena.
Authors: LaComb, L. / Ghosh, A. / Bonanno, J.B. / Nilson, D.J. / Poppel, A.J. / Dada, L. / Cahill, S.M. / Maianti, J.P. / Kitamura, S. / Cowburn, D. / Almo, S.C.
History
DepositionJun 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein enabled homolog
B: poly-proline segment of PTP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2235
Polymers14,0032
Non-polymers2203
Water1,13563
1
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0854
Polymers12,8651
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: poly-proline segment of PTP1B


  • defined by author
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1381
Polymers1,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.654, 49.072, 54.105
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 Protein enabled homolog


Mass: 12864.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N8S7
#2: Protein/peptide poly-proline segment of PTP1B / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 1138.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18031
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.0 M Ammonium sulfate and 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.4→19.83 Å / Num. obs: 21372 / % possible obs: 99.6 % / Redundancy: 12.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.029 / Rrim(I) all: 0.1 / Χ2: 1.01 / Net I/σ(I): 18.8 / Num. measured all: 259048
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.577 / Num. measured all: 12450 / Num. unique obs: 1040 / CC1/2: 0.889 / Rpim(I) all: 0.18 / Rrim(I) all: 0.606 / Χ2: 1.04 / Net I/σ(I) obs: 6.3

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.83 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 1060 4.97 %
Rwork0.1873 --
obs0.1877 21323 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 13 63 978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d1.472
X-RAY DIFFRACTIONf_dihedral_angle_d16.943353
X-RAY DIFFRACTIONf_chiral_restr0.098146
X-RAY DIFFRACTIONf_plane_restr0.013177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.460.29261580.25212468X-RAY DIFFRACTION100
1.46-1.540.23161370.21622456X-RAY DIFFRACTION98
1.54-1.640.20581250.20092496X-RAY DIFFRACTION100
1.64-1.760.23131150.19042531X-RAY DIFFRACTION100
1.76-1.940.19071380.1792486X-RAY DIFFRACTION99
1.94-2.220.20111230.17352556X-RAY DIFFRACTION100
2.22-2.80.18581490.18132554X-RAY DIFFRACTION100
2.8-19.830.17161150.18352716X-RAY DIFFRACTION100

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