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- PDB-4y32: Crystal structure of C-terminal modified Tau peptide-hybrid 109B ... -

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Basic information

Entry
Database: PDB / ID: 4y32
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 109B with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • ARG-THR-PRO-SEP-LEU-PRO-CNC(C(C)O)C(=O)N1CCCC1CCOC
KeywordsSIGNALING PROTEIN / Peptide-hybrid / Inhibitor / Protein-protein interaction / Peptide binding protein / Adapter protein / 14-3-3
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
(2S)-2-(2-methoxyethyl)pyrrolidine / Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBartel, M. / Milroy, L. / Bier, D. / 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 2.0Mar 13, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / database_PDB_remark ...atom_site / database_PDB_remark / diffrn_radiation_wavelength / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_seq_id / _database_PDB_remark.text / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value
Revision 2.1Jan 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
Revision 2.2Oct 23, 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: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: ARG-THR-PRO-SEP-LEU-PRO-CNC(C(C)O)C(=O)N1CCCC1CCOC
D: ARG-THR-PRO-SEP-LEU-PRO-CNC(C(C)O)C(=O)N1CCCC1CCOC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9195
Polymers54,7904
Non-polymers1291
Water13,709761
1
A: 14-3-3 protein sigma
C: ARG-THR-PRO-SEP-LEU-PRO-CNC(C(C)O)C(=O)N1CCCC1CCOC
hetero molecules

B: 14-3-3 protein sigma
D: ARG-THR-PRO-SEP-LEU-PRO-CNC(C(C)O)C(=O)N1CCCC1CCOC


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 area4030 Å2
ΔGint-23 kcal/mol
Surface area23840 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-CNC(C(C)O)C(=O)N1CCCC1CCOC


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


Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99983 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99983 Å / Relative weight: 1
ReflectionResolution: 1.7→47.477 Å / Num. obs: 63066 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.426 % / Biso Wilson estimate: 29.232 Å2 / 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: _

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
XSCALEdata scaling
REFMAC5.6.0017refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FL5

4fl5


Resolution: 1.7→47.477 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.792 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 3178 5 %RANDOM
Rwork0.181 60398 --
obs0.1838 63573 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.43 Å2 / Biso mean: 27.133 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2---0.29 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.7→47.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms103 3683 9 761 4556
Biso mean--35.68 41.94 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024024
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.995453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8155530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9124.815189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49815779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1811529
X-RAY DIFFRACTIONr_chiral_restr0.140.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212995
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 217 -
Rwork0.185 4155 -
all-4372 -
obs--99.95 %

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