[English] 日本語
Yorodumi
- PDB-4y5i: Crystal structure of C-terminal modified Tau peptide-hybrid 126B ... -

+
Open data


ID or keywords:

Loading...

-
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 tauTau protein
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Tau protein / 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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: 0

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more