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- PDB-2on9: Structure of an amyloid forming peptide VQIVYK from the repeat re... -

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Basic information

Entry
Database: PDB / ID: 2on9
TitleStructure of an amyloid forming peptide VQIVYK from the repeat region of Tau
ComponentsVQIVYK peptide corresponding to residues 306-311 in the tau protein
KeywordsPROTEIN FIBRIL / parallel face-to-face-Up/Up beta sheets / steric zipper
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 / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / apolipoprotein binding / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / stress granule assembly / regulation of cellular response to heat / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / SH3 domain binding / cellular response to reactive oxygen species / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding
Similarity search - Function
: / 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.
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSambashivan, S. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A.O. / Riekel, C. / Eisenberg, D.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VQIVYK peptide corresponding to residues 306-311 in the tau protein
B: VQIVYK peptide corresponding to residues 306-311 in the tau protein


Theoretical massNumber of molelcules
Total (without water)1,5002
Polymers1,5002
Non-polymers00
Water1267
1
A: VQIVYK peptide corresponding to residues 306-311 in the tau protein
B: VQIVYK peptide corresponding to residues 306-311 in the tau protein

A: VQIVYK peptide corresponding to residues 306-311 in the tau protein
B: VQIVYK peptide corresponding to residues 306-311 in the tau protein


Theoretical massNumber of molelcules
Total (without water)3,0004
Polymers3,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)4.863, 61.926, 15.413
Angle α, β, γ (deg.)90.000, 98.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide VQIVYK peptide corresponding to residues 306-311 in the tau protein


Mass: 749.917 Da / Num. of mol.: 2 / Fragment: residues 306-311 / Source method: obtained synthetically / Details: Peptide was obtained from CSBio company. / References: UniProt: P10636*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.53 Å3/Da / Density % sol: 19.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peptide concentration: 30mg/ml, peptide:Reservoir ratio 1:1, Reservoir: 0.2M Ammonium acetate, 0.1M HEPES-Na, 45% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.98
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. obs: 1222 / % possible obs: 85.4 % / Redundancy: 2.89 % / Rmerge(I) obs: 0.161 / Χ2: 1.058 / Net I/σ(I): 3.8
Reflection shellResolution: 1.5→1.62 Å / Rmerge(I) obs: 0.489 / Num. unique all: 238 / Χ2: 1.104 / % possible all: 77

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Extended beta strand VQIVYK

Resolution: 1.51→30.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.485 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 59 4.9 %RANDOM
Rwork0.206 ---
obs0.207 1207 85.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.391 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.03 Å2
2---0.14 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.51→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms111 0 0 7 118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023112
X-RAY DIFFRACTIONr_bond_other_d0.0010.0272
X-RAY DIFFRACTIONr_angle_refined_deg1.1972.01152
X-RAY DIFFRACTIONr_angle_other_deg0.7573182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.252512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.032254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41524
X-RAY DIFFRACTIONr_chiral_restr0.0920.220
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02109
X-RAY DIFFRACTIONr_gen_planes_other00.0219
X-RAY DIFFRACTIONr_nbd_refined0.0020.23
X-RAY DIFFRACTIONr_nbd_other0.1780.245
X-RAY DIFFRACTIONr_nbtor_refined0.1830.245
X-RAY DIFFRACTIONr_nbtor_other0.0710.260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.25
X-RAY DIFFRACTIONr_mcbond_it0.621.586
X-RAY DIFFRACTIONr_mcbond_other0.1221.523
X-RAY DIFFRACTIONr_mcangle_it0.7612107
X-RAY DIFFRACTIONr_scbond_it1.11368
X-RAY DIFFRACTIONr_scangle_it1.3324.544
LS refinement shellResolution: 1.51→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 3 -
Rwork0.456 76 -
obs-79 69.3 %

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