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- PDB-5hf3: Crystal structure of C-terminal modified Tau peptide-hybrid 201D ... -

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Basic information

Entry
Database: PDB / ID: 5hf3
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 201D with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • modified Tau peptide
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex / negative regulation of tubulin deacetylation / generation of neurons / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / keratinization / regulation of mitochondrial fission / axon development / central nervous system neuron development / intracellular distribution of mitochondria / regulation of cell-cell adhesion / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / apolipoprotein binding / glial cell projection / phosphoserine residue binding / axolemma / protein polymerization / negative regulation of mitochondrial fission / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / neurofibrillary tangle assembly / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / Activation of AMPK downstream of NMDARs / synapse assembly / regulation of cellular response to heat / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / supramolecular fiber organization / RHO GTPases activate PKNs / positive regulation of protein localization / regulation of calcium-mediated signaling / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / axon cytoplasm / positive regulation of microtubule polymerization / stress granule assembly / phosphatidylinositol binding / positive regulation of cell adhesion / regulation of microtubule cytoskeleton organization / nuclear periphery / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / positive regulation of superoxide anion generation / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / astrocyte activation / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to lead ion / synapse organization / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / intrinsic apoptotic signaling pathway in response to DNA damage / neuron projection development / intracellular protein localization / cell-cell signaling
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 14-3-3 protein sigma / 14-3-3 proteins signature 2. ...14-3-3 domain / Delta-Endotoxin; domain 1 / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBartel, M. / Milroy, L.G. / Brunsveld, L. / Ottmann, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Stabilizer-Guided Inhibition of Protein-Protein Interactions.
Authors: Milroy, L.G. / Bartel, M. / Henen, M.A. / Leysen, S. / Adriaans, J.M. / Brunsveld, L. / Landrieu, I. / Ottmann, C.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.source
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 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: 14-3-3 protein sigma
B: modified Tau peptide


Theoretical massNumber of molelcules
Total (without water)27,6562
Polymers27,6562
Non-polymers00
Water7,620423
1
A: 14-3-3 protein sigma
B: modified Tau peptide

A: 14-3-3 protein sigma
B: modified Tau peptide


Theoretical massNumber of molelcules
Total (without water)55,3124
Polymers55,3124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5270 Å2
ΔGint-32 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.313, 112.467, 62.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26558.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide modified Tau peptide


Mass: 1097.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P10636*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M Hepes/NaOH pH 7.1, 0.19 M CaCl2, 24% PEG 400, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→66.423 Å / Num. obs: 63066 / % possible obs: 99.6 % / Redundancy: 5.6 % / Net I/σ(I): 29.72

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.3.0phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FL5

4fl5


Resolution: 1.8→45.491 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 2000 7.43 %
Rwork0.1656 --
obs0.1686 26915 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.05 Å2 / Biso mean: 13.9833 Å2 / Biso min: 0.9 Å2
Refinement stepCycle: final / Resolution: 1.8→45.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 156 423 2395
Biso mean--23.64 26.03 -
Num. residues----231

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