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- PDB-6fav: Crystal structure of C-terminal modified Tau peptide-hybrid 4.2f-... -

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Basic information

Entry
Database: PDB / ID: 6fav
TitleCrystal structure of C-terminal modified Tau peptide-hybrid 4.2f-I with 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY
  • THR-PRO-SEP-LEU-PRO-GLY
KeywordsSTRUCTURAL PROTEIN / Tau 14-3-3 Alzheimer
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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / 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 / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / positive regulation of cell adhesion / nuclear periphery / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / 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 / synapse organization / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / SH3 domain binding / response to lead ion / 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
Chem-D3Q / Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsAndrei, S.A. / Meijer, F.A. / Ottmann, C. / Milroy, L.G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands
CitationJournal: ACS Chem Neurosci / Year: 2018
Title: Inhibition of 14-3-3/Tau by Hybrid Small-Molecule Peptides Operating via Two Different Binding Modes.
Authors: Andrei, S.A. / Meijer, F.A. / Neves, J.F. / Brunsveld, L. / Landrieu, I. / Ottmann, C. / Milroy, L.G.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Feb 27, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...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_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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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.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.ptnr1_symmetry / _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
Revision 1.4Nov 13, 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: ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY
C: 14-3-3 protein sigma
D: THR-PRO-SEP-LEU-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,29113
Polymers54,5704
Non-polymers7219
Water12,448691
1
A: 14-3-3 protein sigma
B: ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY
hetero molecules

C: 14-3-3 protein sigma
D: THR-PRO-SEP-LEU-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,29113
Polymers54,5704
Non-polymers7219
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area5370 Å2
ΔGint-75 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.789, 70.140, 128.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AC

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


Mass: 26542.914 Da / Num. of mol.: 2
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

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Protein/peptide , 2 types, 2 molecules BD

#2: Protein/peptide ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY


Mass: 833.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#3: Protein/peptide THR-PRO-SEP-LEU-PRO-GLY


Mass: 650.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS

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Non-polymers , 4 types, 700 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-D3Q / (2~{R})-2-[(~{R})-(3-methoxyphenyl)-phenyl-methyl]pyrrolidine


Mass: 267.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21NO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 26% PEG400, 10 mM HEPES pH 7.1, 5% glycerol, 0.19 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.4→47.33 Å / Num. obs: 112108 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.027 / Rrim(I) all: 0.095 / Net I/σ(I): 14.3 / Num. measured all: 1357871 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.4211.81.2276543355290.6210.371.2832.2100
7.67-47.3312.40.04199568000.9990.0120.04343.399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.72 Å47.33 Å
Translation5.72 Å47.33 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.18phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HF3

5hf3


Resolution: 1.4→47.329 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 5606 5.01 %
Rwork0.1444 106400 -
obs0.1457 112006 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.02 Å2 / Biso mean: 22.8227 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 1.4→47.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 47 693 4436
Biso mean--27.48 34.26 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074241
X-RAY DIFFRACTIONf_angle_d0.9085789
X-RAY DIFFRACTIONf_chiral_restr0.061629
X-RAY DIFFRACTIONf_plane_restr0.006772
X-RAY DIFFRACTIONf_dihedral_angle_d21.6321698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.41590.27971730.237134893662
1.4159-1.43260.29451840.220535313715
1.4326-1.450.24471570.204835243681
1.45-1.46840.21471810.189335213702
1.4684-1.48770.21622000.169634943694
1.4877-1.50810.22051840.167934993683
1.5081-1.52960.19741920.162635423734
1.5296-1.55250.20572090.155734453654
1.5525-1.57670.18381690.140735173686
1.5767-1.60260.16151900.130835323722
1.6026-1.63020.16071820.131635253707
1.6302-1.65990.1721650.128935303695
1.6599-1.69180.18581870.128835143701
1.6918-1.72630.16782050.134535033708
1.7263-1.76390.19331770.12935373714
1.7639-1.80490.161700.129335513721
1.8049-1.850.1491710.129735763747
1.85-1.90010.16691990.134334983697
1.9001-1.9560.17021860.133635283714
1.956-2.01910.15371990.130235293728
2.0191-2.09130.17241900.126635553745
2.0913-2.1750.14992030.123935173720
2.175-2.2740.15551760.120835573733
2.274-2.39390.15031980.121635553753
2.3939-2.54390.15132210.122835263747
2.5439-2.74030.16211980.132535863784
2.7403-3.0160.16451800.143935943774
3.016-3.45230.15461740.148936423816
3.4523-4.3490.15651900.142536553845
4.349-47.35590.20781960.187338284024

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