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- PDB-6fau: Crystal structure of C-terminal modified Tau peptide-hybrid 4.2e-... -

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Basic information

Entry
Database: PDB / ID: 6fau
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 4.2e-I 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 / 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
Chem-D3W / 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: 1.25 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 18, 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 1.2Feb 27, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...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_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
Revision 1.4Nov 6, 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: 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)55,33715
Polymers54,5704
Non-polymers76711
Water13,727762
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)55,33715
Polymers54,5704
Non-polymers76711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area5580 Å2
ΔGint-95 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 70.260, 128.180
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, 773 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-D3W / (2~{R})-2-[(~{R})-(2-methoxyphenyl)-phenyl-methyl]pyrrolidine


Mass: 267.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21NO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% PEG400, 10 mM HEPES pH 7.1, 5% glycerol, 0.19 M CaCl2

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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: 1.25→47.35 Å / Num. obs: 157056 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 13.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 13.9 / Num. measured all: 1915223 / Scaling rejects: 246
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.25-1.2712.51.15277240.6920.3371.20199.9
6.85-47.3512.80.05811050.9960.0170.06199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.35 Å47.35 Å
Translation4.35 Å47.35 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.8.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HF3

5hf3


Resolution: 1.25→47.35 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.16
RfactorNum. reflection% reflection
Rfree0.1642 7880 5.02 %
Rwork0.1448 --
obs0.1457 156936 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.13 Å2 / Biso mean: 21.0409 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.25→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 49 763 4516
Biso mean--29.81 32.31 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064392
X-RAY DIFFRACTIONf_angle_d0.8336006
X-RAY DIFFRACTIONf_chiral_restr0.058652
X-RAY DIFFRACTIONf_plane_restr0.005805
X-RAY DIFFRACTIONf_dihedral_angle_d21.0391765
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
1.25-1.26420.24512490.232149385187
1.2642-1.27910.24852430.222549185161
1.2791-1.29470.21442500.213349585208
1.2947-1.31110.22372580.200549115169
1.3111-1.32830.2142700.187548995169
1.3283-1.34650.21132490.182549555204
1.3465-1.36580.20732550.172249245179
1.3658-1.38610.20052850.172748845169
1.3861-1.40780.18672410.165149685209
1.4078-1.43090.1812730.15249165189
1.4309-1.45560.16922370.142749215158
1.4556-1.4820.16342810.131848735154
1.482-1.51050.15612610.127349345195
1.5105-1.54140.13892850.117749455230
1.5414-1.57490.15542610.113849495210
1.5749-1.61150.13912450.113449455190
1.6115-1.65180.14232580.113649885246
1.6518-1.69650.12992530.114149355188
1.6965-1.74640.14712810.121149355216
1.7464-1.80280.16182790.125149445223
1.8028-1.86720.15232950.124849125207
1.8672-1.9420.16492710.132549645235
1.942-2.03040.15882540.127850135267
2.0304-2.13740.14032480.121950115259
2.1374-2.27130.13982860.120549645250
2.2713-2.44670.13422680.125750095277
2.4467-2.69290.1492580.135250415299
2.6929-3.08250.17682640.152850445308
3.0825-3.88340.18152680.151951255393
3.8834-47.38380.17432540.177853335587

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