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- PDB-6fi4: Crystal structure of C-terminal modified Tau peptide-hybrid 3.2e ... -

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Basic information

Entry
Database: PDB / ID: 6fi4
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 3.2e with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • PRO-SEP-LEU-PRO-DVA
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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / 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 / positive regulation of axon extension / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 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 / positive regulation of superoxide anion generation / RHO GTPases activate PKNs / regulation of long-term synaptic depression / positive regulation of protein localization / supramolecular fiber organization / cellular response to brain-derived neurotrophic factor stimulus / 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
(2~{S})-2-(diphenylmethyl)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: 2 Å
AuthorsAndrei, S.A. / Meijer, F.A. / Ottmann, C. / Milroy, L.G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchECHO-STIP 717.014.001 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
DepositionJan 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 28, 2018Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_database_proc
Item: _atom_site.occupancy / _citation.journal_volume ..._atom_site.occupancy / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.1Apr 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 2.2Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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: PRO-SEP-LEU-PRO-DVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4706
Polymers27,1352
Non-polymers3364
Water2,396133
1
A: 14-3-3 protein sigma
B: PRO-SEP-LEU-PRO-DVA
hetero molecules

A: 14-3-3 protein sigma
B: PRO-SEP-LEU-PRO-DVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,94112
Polymers54,2694
Non-polymers6728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area4980 Å2
ΔGint-74 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.380, 148.460, 78.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 26542.914 Da / Num. of mol.: 1
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 PRO-SEP-LEU-PRO-DVA


Mass: 591.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS

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Non-polymers , 5 types, 137 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-60H / (2~{S})-2-(diphenylmethyl)pyrrolidine


Mass: 237.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 25% PEG400, 20 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: 2→74.23 Å / Num. obs: 24922 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 39.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 21.2 / Num. measured all: 308845 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.0512.81.10917930.8240.3221.156100
8.94-74.2312.40.0313270.9990.0090.03299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.93 Å74.23 Å
Translation4.93 Å74.23 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
Starting model: 5hf3

5hf3


Resolution: 2→74.23 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.32
RfactorNum. reflection% reflection
Rfree0.2291 1209 4.85 %
Rwork0.2001 --
obs0.2015 24916 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.89 Å2 / Biso mean: 59.6978 Å2 / Biso min: 34.75 Å2
Refinement stepCycle: final / Resolution: 2→74.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 21 133 1942
Biso mean--80.51 54.29 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031866
X-RAY DIFFRACTIONf_angle_d0.52511
X-RAY DIFFRACTIONf_chiral_restr0.031277
X-RAY DIFFRACTIONf_plane_restr0.002321
X-RAY DIFFRACTIONf_dihedral_angle_d15.9611154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.08010.33261260.295825902716
2.0801-2.17480.30341270.240226032730
2.1748-2.28950.2071290.219625982727
2.2895-2.43290.2841300.206226092739
2.4329-2.62080.21991530.210226042757
2.6208-2.88450.23431240.22226252749
2.8845-3.30190.26781250.219526482773
3.3019-4.16010.2371450.182826592804
4.1601-74.28110.19131500.1827712921
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.46191.5799-0.92326.92833.46113.8233-0.46-0.89680.7202-0.0987-0.1145-1.0639-0.22660.6889-0.17710.57020.02170.09130.379-0.07060.4441-8.3779-13.201514.436
27.962-4.44952.33054.6656-4.20626.55390.03440.12010.13070.1831-0.034-0.06120.18970.1639-0.03390.4655-0.00070.02770.2422-0.0630.29958.1863-28.428412.5133
35.0599-0.60045.20491.9377-0.2997.957-0.097-0.27410.17190.1819-0.12270.08520.2065-0.47290.24240.4312-0.01950.11260.3364-0.090.3616-8.9073-25.55658.307
46.7518-0.74324.20733.4861-0.12627.23840.0101-0.6643-0.05270.3932-0.22570.21490.2881-0.93750.19390.5501-0.11780.16930.5296-0.0870.4032-11.1988-24.956520.7485
54.41171.86010.94634.18871.62524.6663-0.2955-0.12740.06050.1981-0.2450.3996-0.2077-0.83290.53950.49570.07890.12810.5395-0.12120.3575-12.4392-10.704125.2958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 8 )B4 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid -4 through 32 )A-4 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 106 )A33 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 143 )A107 - 143
5X-RAY DIFFRACTION5chain 'A' and (resid 144 through 231 )A144 - 231

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