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- PDB-5btv: Crystal structure of human 14-3-3 sigma in complex with a Tau-pro... -

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Basic information

Entry
Database: PDB / ID: 5btv
TitleCrystal structure of human 14-3-3 sigma in complex with a Tau-protein peptide surrounding pS324
Components
  • 14-3-3 protein sigma
  • Microtubule-associated protein tau - peptide pS324
KeywordsSTRUCTURAL PROTEIN / Peptide binding protein / 14-3-3 / Tau-protein
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / lipoprotein particle binding / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / regulation of epidermal cell division / central nervous system neuron development / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / regulation of microtubule polymerization / keratinocyte development / keratinization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / apolipoprotein binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / protein polymerization / negative regulation of mitochondrial fission / axolemma / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of keratinocyte proliferation / positive regulation of axon extension / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / supramolecular fiber organization / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / regulation of cellular response to heat / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / protein export from nucleus / negative regulation of innate immune response / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of superoxide anion generation / positive regulation of protein export from nucleus / protein phosphatase 2A binding / regulation of autophagy / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / astrocyte activation / TP53 Regulates Metabolic Genes / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / negative regulation of protein kinase activity / PKR-mediated signaling / protein homooligomerization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / : / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / 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, tubulin-binding repeat / Microtubule-associated protein Tau / 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 / Resolution: 1.7 Å
AuthorsOttmann, C. / Schumacher, B. / Bartel, M.
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 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / 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

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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
P: Microtubule-associated protein tau - peptide pS324
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0126
Polymers26,8882
Non-polymers1244
Water5,693316
1
A: 14-3-3 protein sigma
P: Microtubule-associated protein tau - peptide pS324
hetero molecules

A: 14-3-3 protein sigma
P: Microtubule-associated protein tau - peptide pS324
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,02512
Polymers53,7764
Non-polymers2488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3860 Å2
ΔGint-77 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.550, 112.310, 62.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

MG

21A-456-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 26475.828 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 Microtubule-associated protein tau - peptide pS324


Mass: 412.333 Da / Num. of mol.: 1 / Fragment: residues 323-326 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS

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Non-polymers , 4 types, 320 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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
ReflectionResolution: 1.7→10 Å / Num. obs: 31463 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.379 % / Biso Wilson estimate: 22.595 Å2 / Rmerge F obs: 0.079 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.05 / Χ2: 0.95 / Net I/σ(I): 22.03 / Num. measured all: 125780
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.3330.2455.3919000501349840.28599.4
1.8-20.1930.1468.8628052730872400.16899.1
2-2.50.0690.0620.3237872964394680.06998.2
2.5-30.0340.03632.0517114429441500.04196.6
3-40.0190.02546.1413768345432680.02894.6
4-60.0160.02352.577098181516670.02691.8
6-100.0160.02155.0623546295540.02488.1
100.0110.0260.675221941320.02268

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
REFMAC5.5.0102refinement
RefinementResolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.1883 / WRfactor Rwork: 0.1494 / FOM work R set: 0.8831 / SU B: 1.705 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0919 / SU Rfree: 0.0969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1574 5 %RANDOM
Rwork0.1599 ---
obs0.162 29888 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.36 Å2 / Biso mean: 16.626 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 4 316 2136
Biso mean--22.33 29.88 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222026
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9882777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2835.068293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10924.79296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98315.038400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6041515
X-RAY DIFFRACTIONr_chiral_restr0.1640.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021536
X-RAY DIFFRACTIONr_mcbond_it1.3541.51248
X-RAY DIFFRACTIONr_mcangle_it2.2322033
X-RAY DIFFRACTIONr_scbond_it3.7873778
X-RAY DIFFRACTIONr_scangle_it5.8754.5711
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 117 -
Rwork0.216 2214 -
all-2331 -
obs--100 %

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