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- PDB-4y5i: Crystal structure of C-terminal modified Tau peptide-hybrid 126B ... -

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Basic information

Entry
Database: PDB / ID: 4y5i
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 126B with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • Microtubule-associated protein tau
KeywordsSIGNALING PROTEIN / 14-3-3 sigma / protein-protein interaction / inhibitor / tau / peptide-hybrid
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 / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / somatodendritic compartment / positive regulation of microtubule polymerization / axon cytoplasm / astrocyte activation / phosphatidylinositol binding / stress granule assembly / positive regulation of cell adhesion / nuclear periphery / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / 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 / protein homooligomerization / synapse organization / regulation of synaptic plasticity / PKR-mediated signaling / response to lead ion / SH3 domain binding / 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
Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLeysen, S. / Bartel, M. / Milroy, L. / Brunsveld, L. / Ottmann, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Stabilizer-Guided Inhibition of Protein-Protein Interactions.
Authors: Milroy, L.G. / Bartel, M. / Henen, M.A. / Leysen, S. / Adriaans, J.M. / Brunsveld, L. / Landrieu, I. / Ottmann, C.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0Mar 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site / struct_site_gen
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_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 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: 14-3-3 protein sigma
F: Microtubule-associated protein tau
G: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0476
Polymers54,9764
Non-polymers712
Water13,385743
1
A: 14-3-3 protein sigma
F: Microtubule-associated protein tau
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)55,0476
Polymers54,9764
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area4610 Å2
ΔGint-48 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.105, 70.213, 129.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26542.914 Da / Num. of mol.: 2 / Fragment: UNP residues 1-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Details (production host): pProEx Htb / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 945.031 Da / Num. of mol.: 2 / Fragment: UNP residues 528-534 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M Hepes/NaOH pH 7.1, 0.19 M CaCl2, 24% PEG 400, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99983 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99983 Å / Relative weight: 1
ReflectionResolution: 1.4→64.553 Å / Num. all: 113518 / Num. obs: 113518 / % possible obs: 100 % / Redundancy: 13.2 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.081 / Rsym value: 0.077 / Net I/av σ(I): 3.853 / Net I/σ(I): 17.7 / Num. measured all: 1497659
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.4813.20.761216271163800.2170.763.9100
1.48-1.5712.50.4451.6193990155260.130.4456.1100
1.57-1.6713.40.2722.7196586146280.0770.2729.1100
1.67-1.8113.50.1794.1183610136240.050.17912.3100
1.81-1.9812.70.1185.9159351125680.0350.11816.8100
1.98-2.2113.90.088.2158751114100.0220.0825.6100
2.21-2.5613.50.0679.5136763101170.0190.06730.9100
2.56-3.1312.90.0629.511175686300.0180.06234.5100
3.13-4.4313.60.0599.69152767380.0170.05941.4100
4.43-46.93412.60.0696.24905438970.020.06939.999.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FL5

4fl5


Resolution: 1.4→45.125 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 15.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1716 5678 5.01 %
Rwork0.147 107744 -
obs0.1483 113422 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.4 Å2 / Biso mean: 23.1811 Å2 / Biso min: 10.49 Å2
Refinement stepCycle: final / Resolution: 1.4→45.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 114 743 4439
Biso mean--29.82 36.06 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054046
X-RAY DIFFRACTIONf_angle_d0.965530
X-RAY DIFFRACTIONf_chiral_restr0.036625
X-RAY DIFFRACTIONf_plane_restr0.004711
X-RAY DIFFRACTIONf_dihedral_angle_d14.051635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.41590.23322140.17535143728
1.4159-1.43260.18721650.165435723737
1.4326-1.45010.21561810.156335253706
1.4501-1.46840.2071590.144736353794
1.4684-1.48770.1881620.13435393701
1.4877-1.50810.16641770.132535633740
1.5081-1.52970.1722050.127335313736
1.5297-1.55250.16021820.125735733755
1.5525-1.57680.16441920.123335763768
1.5768-1.60260.16262030.116835293732
1.6026-1.63020.16211670.116135853752
1.6302-1.65990.17821800.120535813761
1.6599-1.69180.1531980.122235283726
1.6918-1.72630.17131890.128135533742
1.7263-1.76390.18981870.132935803767
1.7639-1.80490.16122200.135635703790
1.8049-1.85010.18771980.138535593757
1.8501-1.90010.17721870.139835803767
1.9001-1.9560.15972040.143335573761
1.956-2.01910.16111890.136735693758
2.0191-2.09130.15061930.13435843777
2.0913-2.1750.16531970.133735963793
2.175-2.2740.16081800.137536063786
2.274-2.39390.16521810.143136233804
2.3939-2.54390.171780.148236443822
2.5439-2.74030.17851980.157935983796
2.7403-3.0160.15952010.162136513852
3.016-3.45220.18581850.156536513836
3.4522-4.34890.15511920.140237133905
4.3489-45.14880.19282140.177838594073

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