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- PDB-4fl5: Crystal structure of human 14-3-3 sigma in complex with a Tau-pro... -

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Basic information

Entry
Database: PDB / ID: 4fl5
TitleCrystal structure of human 14-3-3 sigma in complex with a Tau-protein peptide surrounding pS214
Components
  • 14-3-3 protein sigma
  • Microtubule-associated protein tau
KeywordsSIGNALING PROTEIN / Peptide binding protein
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
Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSchumacher, B. / Ottmann, C.
CitationJournal: FASEB J. / Year: 2015
Title: Involvement of 14-3-3 in tubulin instability and impaired axon development is mediated by Tau.
Authors: Joo, Y. / Schumacher, B. / Landrieu, I. / Bartel, M. / Smet-Nocca, C. / Jang, A. / Choi, H.S. / Jeon, N.L. / Chang, K.A. / Kim, H.S. / Ottmann, C. / Suh, Y.H.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Data collection
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: 14-3-3 protein sigma
P: Microtubule-associated protein tau
Q: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,06919
Polymers55,3844
Non-polymers68515
Water9,530529
1
A: 14-3-3 protein sigma
P: Microtubule-associated protein tau
hetero molecules

B: 14-3-3 protein sigma
Q: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,06919
Polymers55,3844
Non-polymers68515
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area5580 Å2
ΔGint-107 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.690, 70.080, 128.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe second part of the biological assembly is generated by the two fold axis: x-1/2,-y-1/2,-z.

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABPQ

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


Mass: 26558.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, SFN / Plasmid: pProEx HtB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P31947
#2: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1133.168 Da / Num. of mol.: 2 / Fragment: UNP residues 527-536 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636

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Non-polymers , 5 types, 544 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes/NaOH pH 7.5, 0.2 M CaCl2, 28% PEG 400, 5% glycerol, 2 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 175180 / Rmerge(I) obs: 0.047 / D res high: 1.9 Å / Num. obs: 45097 / % possible obs: 99.6
Diffraction reflection shellHighest resolution: 1.9 Å / Lowest resolution: 2 Å / Num. obs: 6338 / % possible obs: 99.5 % / Rmerge(I) obs: 0.233
ReflectionResolution: 1.9→19.643 Å / Num. all: 45268 / Num. obs: 45097 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.532 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-20.2335.8823457633899.5
2-2.20.13110.0936034946799.6
2.2-2.50.07916.2636185919199.7
2.5-30.05123.6433278834699.9
3-3.50.03235.2617111429599.9
3.5-40.02545.669563240399.8
4-60.02346.5713887352999.9
6-100.02248.794583121499.8
10-120.01960.56539151100
120.01854.7254316374.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.64 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2117 / WRfactor Rwork: 0.1561 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8809 / SU B: 2.712 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1332 / SU Rfree: 0.1355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 2255 5 %RANDOM
Rwork0.1561 ---
obs0.1589 45096 100 %-
all-45097 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.87 Å2 / Biso mean: 17.8038 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.56 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 30 529 4254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224274
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9935885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.5775.097618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46124.641209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00515.036831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6021536
X-RAY DIFFRACTIONr_chiral_restr0.1510.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213290
X-RAY DIFFRACTIONr_mcbond_it1.2771.52609
X-RAY DIFFRACTIONr_mcangle_it2.08124273
X-RAY DIFFRACTIONr_scbond_it3.22131665
X-RAY DIFFRACTIONr_scangle_it4.9194.51531
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 163 -
Rwork0.18 3102 -
all-3265 -
obs-42841 100 %

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