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- PDB-6fby: Crystal structure of C-terminal modified Tau peptide-hybrid 4.2b ... -

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Basic information

Entry
Database: PDB / ID: 6fby
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 4.2b with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY
  • THR-PRO-SEP-LEU-PRO-GLY
KeywordsSTRUCTURAL PROTEIN / Tau 14-3-3 Alzheimer
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / microtubule stabilizing activity / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of epidermal cell differentiation / tubulin complex / positive regulation of protein localization to synapse / regulation of epidermal cell division ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / microtubule stabilizing activity / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of epidermal cell differentiation / tubulin complex / positive regulation of protein localization to synapse / regulation of epidermal cell division / protein kinase C inhibitor activity / phosphatidylinositol bisphosphate binding / generation of neurons / axonal transport of mitochondrion / axon development / rRNA metabolic process / central nervous system neuron development / regulation of microtubule-based movement / negative regulation of protein localization to mitochondrion / regulation of mitochondrial fission / positive regulation of hippo signaling / regulation of cell-cell adhesion / regulation of chromosome organization / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / negative regulation of mitochondrial membrane potential / microtubule polymerization / establishment of skin barrier / regulation of microtubule polymerization / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / dynactin binding / apolipoprotein binding / positive regulation of keratinocyte differentiation / regulation of calcium-mediated signaling / main axon / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Caspase-mediated cleavage of cytoskeletal proteins / glial cell projection / negative regulation of protein localization to plasma membrane / regulation of microtubule polymerization or depolymerization / cAMP/PKA signal transduction / protein export from nucleus / neurofibrillary tangle assembly / negative regulation of mitochondrial fission / protein polymerization / positive regulation of axon extension / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / axolemma / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / release of cytochrome c from mitochondria / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of protein kinase activity / regulation of cellular response to heat / positive regulation of microtubule polymerization / positive regulation of protein export from nucleus / positive regulation of superoxide anion generation / cytoplasmic microtubule organization / Activation of AMPK downstream of NMDARs / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / axon cytoplasm / keratinocyte differentiation / positive regulation of protein localization / supramolecular fiber organization / synapse assembly / somatodendritic compartment / astrocyte activation / positive regulation of cell adhesion / nuclear periphery / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / phosphatidylinositol binding / protein phosphatase 2A binding / stress granule assembly / enzyme inhibitor activity / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / SH3 domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to reactive oxygen species / regulation of microtubule cytoskeleton organization / microtubule cytoskeleton organization / microglial cell activation / cellular response to nerve growth factor stimulus / memory / Hsp90 protein binding / regulation of autophagy / regulation of synaptic plasticity / protein sequestering activity / protein homooligomerization / synapse organization / PKR-mediated signaling / response to lead ion / neuron projection development / intracellular protein localization / cytoplasmic ribonucleoprotein granule
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
Chem-D4H / 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: 1.5 Å
AuthorsAndrei, S.A. / Meijer, F.A. / Ottmann, C. / Milroy, L.G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands
CitationJournal: ACS Chem Neurosci / Year: 2018
Title: Inhibition of 14-3-3/Tau by Hybrid Small-Molecule Peptides Operating via Two Different Binding Modes.
Authors: Andrei, S.A. / Meijer, F.A. / Neves, J.F. / Brunsveld, L. / Landrieu, I. / Ottmann, C. / Milroy, L.G.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Feb 27, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
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 / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_struct_assembly_prop.value
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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: ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY
C: 14-3-3 protein sigma
D: THR-PRO-SEP-LEU-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,23612
Polymers54,5704
Non-polymers6668
Water12,935718
1
A: 14-3-3 protein sigma
B: ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY
hetero molecules

C: 14-3-3 protein sigma
D: THR-PRO-SEP-LEU-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,23612
Polymers54,5704
Non-polymers6668
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area5330 Å2
ΔGint-76 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.759, 70.230, 127.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AC

#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

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Protein/peptide , 2 types, 2 molecules BD

#2: Protein/peptide ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY


Mass: 833.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#3: Protein/peptide THR-PRO-SEP-LEU-PRO-GLY


Mass: 650.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS

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Non-polymers , 4 types, 726 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-D4H / (2~{R})-2-[(~{S})-(3-methylphenyl)-phenyl-methyl]pyrrolidine


Mass: 251.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21N / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 24% PEG400, 10 mM HEPES pH 7.1, 5% glycerol, 0.19 M CaCl 2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.5→46.8 Å / Num. obs: 91278 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 15.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.03 / Rrim(I) all: 0.104 / Net I/σ(I): 15.2 / Num. measured all: 1117687 / Scaling rejects: 185
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5312.41.1895560744710.6770.351.242.3100
8.22-46.812.30.03981906640.9990.0110.0451.399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.72 Å46.8 Å
Translation5.72 Å46.8 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.18phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.797 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 4551 4.99 %
Rwork0.1405 86644 -
obs0.1425 91195 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.16 Å2 / Biso mean: 23.4895 Å2 / Biso min: 7.89 Å2
Refinement stepCycle: final / Resolution: 1.5→46.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 44 718 4450
Biso mean--29.99 35.41 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084252
X-RAY DIFFRACTIONf_angle_d0.855803
X-RAY DIFFRACTIONf_chiral_restr0.044635
X-RAY DIFFRACTIONf_plane_restr0.005768
X-RAY DIFFRACTIONf_dihedral_angle_d16.0872707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5170.25251410.205328442985
1.517-1.53490.26751510.206828583009
1.5349-1.55360.25491460.198828442990
1.5536-1.57330.2461580.174828623020
1.5733-1.5940.21961430.165628402983
1.594-1.61580.22871420.160828883030
1.6158-1.63890.21761340.151828713005
1.6389-1.66340.2021390.150328452984
1.6634-1.68940.21811670.14328743041
1.6894-1.71710.17891590.143928392998
1.7171-1.74670.22221580.13528713029
1.7467-1.77840.17251570.129628392996
1.7784-1.81260.16791540.127828483002
1.8126-1.84960.17991450.124329163061
1.8496-1.88990.17311200.132428712991
1.8899-1.93380.18181610.127128372998
1.9338-1.98220.15741640.123628683032
1.9822-2.03580.1741400.122729003040
2.0358-2.09570.17331700.120828803050
2.0957-2.16330.14961630.117628673030
2.1633-2.24060.17491550.114728803035
2.2406-2.33040.1541470.112328963043
2.3304-2.43640.15981720.112128673039
2.4364-2.56490.14061490.117829073056
2.5649-2.72550.16341570.125628963053
2.7255-2.93590.17441620.134729243086
2.9359-3.23130.20241470.14329183065
3.2313-3.69880.16681340.144629823116
3.6988-4.65940.16991530.135929883141
4.6594-46.81930.20151630.19931243287

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