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- PDB-4y3b: Crystal structure of C-terminal modified Tau peptide-hybrid 201D ... -

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Basic information

Entry
Database: PDB / ID: 4y3b
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 201D with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • ARG-THR-PRO-SEP-LEU-PRO-THR-[H][C@@]1(C(C2=CC=CC=C2)C3=CC=CC=C3)CCCN1C
KeywordsSIGNALING PROTEIN / 14-3-3 FOLD / Tau / ALL ALPHA-HELICAL / ADAPTER PROTEIN / PROTEIN-PROTEIN INTERACTION / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / regulation of epidermal cell division / protein kinase C inhibitor activity / central nervous system neuron development / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / apolipoprotein binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / protein polymerization / negative regulation of mitochondrial fission / axolemma / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / establishment of skin barrier / positive regulation of axon extension / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / supramolecular fiber organization / stress granule assembly / regulation of cellular response to heat / cytoplasmic microtubule organization / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / axon cytoplasm / RHO GTPases activate PKNs / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / protein kinase A signaling / protein export from nucleus / negative regulation of innate immune response / phosphatidylinositol binding / nuclear periphery / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / cellular response to nerve growth factor stimulus / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / astrocyte activation / TP53 Regulates Metabolic Genes / response to lead ion / synapse organization / microglial cell activation / negative regulation of protein kinase activity / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / : / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / 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, tubulin-binding repeat / Microtubule-associated protein Tau / 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
(2S)-2-(2-methoxyethyl)pyrrolidine / Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Mar 13, 2019Group: Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_assembly ...diffrn_radiation_wavelength / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: ARG-THR-PRO-SEP-LEU-PRO-THR-[H][C@@]1(C(C2=CC=CC=C2)C3=CC=CC=C3)CCCN1C
D: ARG-THR-PRO-SEP-LEU-PRO-THR-[H][C@@]1(C(C2=CC=CC=C2)C3=CC=CC=C3)CCCN1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9195
Polymers54,7904
Non-polymers1291
Water12,376687
1
A: 14-3-3 protein sigma
C: ARG-THR-PRO-SEP-LEU-PRO-THR-[H][C@@]1(C(C2=CC=CC=C2)C3=CC=CC=C3)CCCN1C
hetero molecules

B: 14-3-3 protein sigma
D: ARG-THR-PRO-SEP-LEU-PRO-THR-[H][C@@]1(C(C2=CC=CC=C2)C3=CC=CC=C3)CCCN1C


Theoretical massNumber of molelcules
Total (without water)54,9195
Polymers54,7904
Non-polymers1291
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area4080 Å2
ΔGint-25 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.062, 70.283, 128.778
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26542.914 Da / Num. of mol.: 2
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 ARG-THR-PRO-SEP-LEU-PRO-THR-[H][C@@]1(C(C2=CC=CC=C2)C3=CC=CC=C3)CCCN1C


Mass: 851.861 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The C-terminal proline contains chemical modifications
Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#3: Chemical ChemComp-49F / (2S)-2-(2-methoxyethyl)pyrrolidine


Mass: 129.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.6 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 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge F obs: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.044 / Χ2: 1.013 / Net I/σ(I): 29.72 / Num. measured all: 408200
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.9640.327.0864753982098070.34899.9
1.8-1.90.9830.21810.5753067788578810.23799.9
1.9-20.9910.1514.7241473640063970.163100
2-2.10.9950.120.4233544523352300.10999.9
2.1-2.20.9970.07426.5829734433243280.0899.9
2.2-2.40.9980.05733.0445098668566830.062100
2.4-2.80.9990.04240.6653163833183170.04699.8
2.8-3.20.9990.03251.5830718471246880.03599.5
3.2-3.50.9990.02757.3313705228222660.0399.3
3.5-40.9990.02560.4113377243424160.02799.3
4-4.20.9990.02366.9842336856790.02599.1
4.2-4.70.9990.02266.367491123712280.02499.3
4.7-50.9990.02366.4631725335290.02599.2
50.9990.02363.7914672272026170.02596.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å46.94 Å
Translation1.7 Å46.94 Å

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Processing

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

4fl5


Resolution: 1.8→45.491 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.99 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 3178 5 %
Rwork0.1646 60395 -
obs0.166 26915 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.99 Å2 / Biso mean: 25.9192 Å2 / Biso min: 10.63 Å2
Refinement stepCycle: final / Resolution: 1.8→45.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 9 687 4444
Biso mean--44.22 36.32 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093970
X-RAY DIFFRACTIONf_angle_d1.1825381
X-RAY DIFFRACTIONf_chiral_restr0.086602
X-RAY DIFFRACTIONf_plane_restr0.004695
X-RAY DIFFRACTIONf_dihedral_angle_d13.2581582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72540.24321360.1942581100
1.7254-1.75230.22291370.18712602100
1.7523-1.78110.23851370.17382597100
1.7811-1.81180.23311370.1762606100
1.8118-1.84470.18911360.17042588100
1.8447-1.88020.20361360.1692602100
1.8802-1.91860.19871370.17092602100
1.9186-1.96030.19281380.16672613100
1.9603-2.00590.20171370.16072606100
2.0059-2.05610.20341370.1652599100
2.0561-2.11170.22141370.1572605100
2.1117-2.17380.181380.15462612100
2.1738-2.2440.19841380.15262617100
2.244-2.32420.17951370.15632615100
2.3242-2.41720.20651390.15772629100
2.4172-2.52720.1871380.16252627100
2.5272-2.66050.17921390.16662624100
2.6605-2.82710.18441380.17312632100
2.8271-3.04540.19831390.17282644100
3.0454-3.35180.1991390.1697265299
3.3518-3.83660.18731390.1574263899
3.8366-4.8330.15971430.1443270399
4.8330.20981460.1838280198

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