[English] 日本語
Yorodumi
- PDB-5btv: Crystal structure of human 14-3-3 sigma in complex with a Tau-pro... -

+
Open data


ID or keywords:

Loading...

-
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 / histone-dependent DNA binding / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of epidermal cell differentiation / tubulin complex / positive regulation of protein localization to synapse / regulation of epidermal cell division / protein kinase C inhibitor activity ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of epidermal cell differentiation / tubulin complex / positive regulation of protein localization to synapse / regulation of epidermal cell division / protein kinase C inhibitor activity / phosphatidylinositol bisphosphate binding / generation of neurons / axonal transport of mitochondrion / axon development / rRNA metabolic process / central nervous system neuron development / regulation of microtubule-based movement / negative regulation of protein localization to mitochondrion / regulation of mitochondrial fission / regulation of cell-cell adhesion / regulation of chromosome organization / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / establishment of skin barrier / regulation of microtubule polymerization / Regulation of localization of FOXO transcription factors / Regulation of GBP-mediated host defense / dynactin binding / apolipoprotein binding / regulation of calcium-mediated signaling / main axon / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Caspase-mediated cleavage of cytoskeletal proteins / glial cell projection / negative regulation of protein localization to plasma membrane / regulation of microtubule polymerization or depolymerization / cAMP/PKA signal transduction / neurofibrillary tangle assembly / protein export from nucleus / negative regulation of mitochondrial fission / protein polymerization / positive regulation of axon extension / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / axolemma / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / release of cytochrome c from mitochondria / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of protein kinase activity / positive regulation of microtubule polymerization / regulation of cellular response to heat / positive regulation of protein export from nucleus / positive regulation of superoxide anion generation / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule organization / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / axon cytoplasm / positive regulation of protein localization / supramolecular fiber organization / synapse assembly / somatodendritic compartment / astrocyte activation / positive regulation of cell adhesion / nuclear periphery / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / phosphatidylinositol binding / protein phosphatase 2A binding / enzyme inhibitor activity / stress granule assembly / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / SH3 domain binding / cellular response to reactive oxygen species / regulation of microtubule cytoskeleton organization / memory / microglial cell activation / cellular response to nerve growth factor stimulus / regulation of synaptic plasticity / Hsp90 protein binding / microtubule cytoskeleton organization / regulation of autophagy / protein sequestering activity / synapse organization / protein homooligomerization / PKR-mediated signaling / response to lead ion / neuron projection development / intracellular protein localization / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / regulation of protein localization / cell-cell signaling / positive regulation of cell growth
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 / 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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...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 / 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.ptnr2_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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: _

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

-
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 %

+
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