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- PDB-6fbw: Crystal structure of C-terminal modified Tau peptide-hybrid 4.2f-... -

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Basic information

Entry
Database: PDB / ID: 6fbw
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 4.2f-II with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • ARG-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 / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding ...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 / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / generation of neurons / regulation of epidermal cell division / protein kinase C inhibitor activity / rRNA metabolic process / axonal transport of mitochondrion / positive regulation of epidermal cell differentiation / keratinocyte development / regulation of mitochondrial fission / keratinization / axon development / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / regulation of cell-cell adhesion / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / dynactin binding / regulation of microtubule polymerization / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / apolipoprotein binding / main axon / keratinocyte proliferation / protein polymerization / axolemma / glial cell projection / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of keratinocyte proliferation / establishment of skin barrier / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / negative regulation of protein localization to plasma membrane / neurofibrillary tangle assembly / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of axon extension / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / positive regulation of cell adhesion / nuclear periphery / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / regulation of microtubule cytoskeleton organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / synapse organization / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / SH3 domain binding / response to lead ion / microtubule cytoskeleton organization / memory / 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-D4K / 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: 1.45 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 2.1Jan 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_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 2.2Oct 9, 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: ARG-THR-PRO-SEP-LEU-PRO-GLY
C: 14-3-3 protein sigma
D: ARG-THR-PRO-SEP-LEU-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39912
Polymers54,7014
Non-polymers6988
Water12,070670
1
A: 14-3-3 protein sigma
B: ARG-THR-PRO-SEP-LEU-PRO-GLY
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)55,39912
Polymers54,7014
Non-polymers6988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area5220 Å2
ΔGint-80 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.878, 70.240, 128.459
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 / Protein/peptide , 2 types, 4 molecules ACBD

#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-GLY


Mass: 807.809 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS

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Non-polymers , 4 types, 678 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-D4K / (2~{R})-2-[(~{S})-(3-methoxyphenyl)-phenyl-methyl]pyrrolidine


Mass: 267.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 52.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 24% PEG400, 10 mM HEPES pH 7.3, 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: 1.45→47.4 Å / Num. obs: 101490 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 16.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Net I/σ(I): 17.7 / Num. measured all: 1253770 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.45-1.4712.61.26349760.6330.371.316100
7.94-47.412.40.0327220.9990.0090.03399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.71 Å47.4 Å
Translation5.71 Å47.4 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.18phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HF3

5hf3


Resolution: 1.45→47.4 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.11
RfactorNum. reflection% reflection
Rfree0.1784 4989 4.92 %
Rwork0.1511 --
obs0.1525 101399 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.32 Å2 / Biso mean: 25.7166 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 1.45→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 46 670 4389
Biso mean--26.73 35.94 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074179
X-RAY DIFFRACTIONf_angle_d0.8735708
X-RAY DIFFRACTIONf_chiral_restr0.057629
X-RAY DIFFRACTIONf_plane_restr0.005750
X-RAY DIFFRACTIONf_dihedral_angle_d19.0591662
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
1.45-1.46650.28741710.233131453316
1.4665-1.48370.24441500.218731843334
1.4837-1.50180.24671490.209132123361
1.5018-1.52080.24111740.195931773351
1.5208-1.54090.21871660.194431583324
1.5409-1.5620.22661750.192231823357
1.562-1.58430.25281840.177631423326
1.5843-1.60790.19181810.169431793360
1.6079-1.63310.20941570.172231943351
1.6331-1.65980.18551570.157331843341
1.6598-1.68850.18731720.151131753347
1.6885-1.71920.18421630.150131733336
1.7192-1.75220.18711670.144232303397
1.7522-1.7880.18661510.146431933344
1.788-1.82690.17791770.141831443321
1.8269-1.86940.18271570.138332163373
1.8694-1.91610.16941730.141932043377
1.9161-1.96790.15571540.142832243378
1.9679-2.02580.17612020.138431473349
2.0258-2.09120.17861550.135432383393
2.0912-2.1660.16611670.131532083375
2.166-2.25270.15291660.12832313397
2.2527-2.35520.14821730.126331923365
2.3552-2.47940.17361640.133832383402
2.4794-2.63470.16991690.133332183387
2.6347-2.83810.17511430.142532723415
2.8381-3.12370.17881730.150832633436
3.1237-3.57550.15861630.149232893452
3.5755-4.50430.15791680.138333223490
4.5043-47.4250.20011680.190534763644

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