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- PDB-4np8: Structure of an amyloid forming peptide VQIVYK from the second re... -

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Basic information

Entry
Database: PDB / ID: 4np8
TitleStructure of an amyloid forming peptide VQIVYK from the second repeat region of tau (alternate polymorph)
ComponentsMicrotubule-associated protein tau
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
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 / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / 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 / apolipoprotein binding / main axon / protein polymerization / axolemma / glial cell projection / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / neurofibrillary tangle assembly / positive regulation of axon extension / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / supramolecular fiber organization / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / nuclear periphery / regulation of microtubule cytoskeleton organization / protein phosphatase 2A binding / cellular response to reactive oxygen species / 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 / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / actin binding / microtubule cytoskeleton / cell body / growth cone / double-stranded DNA binding / protein-macromolecule adaptor activity / microtubule binding / dendritic spine / sequence-specific DNA binding / amyloid fibril formation / microtubule / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
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. / :
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsLandau, M. / Eisenberg, D. / Sawaya, M.R. / Dannenberg, J. / Kobko, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Molecular mechanisms for protein-encoded inheritance.
Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionDec 18, 2013ID: 3FQP
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)7501
Polymers7501
Non-polymers00
Water181
1
A: Microtubule-associated protein tau
x 8


Theoretical massNumber of molelcules
Total (without water)5,9998
Polymers5,9998
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
crystal symmetry operation4_465-x-1/2,y+3/2,-z1
crystal symmetry operation4_475-x-1/2,y+5/2,-z1
crystal symmetry operation4_485-x-1/2,y+7/2,-z1
Unit cell
Length a, b, c (Å)28.635, 4.880, 35.807
Angle α, β, γ (deg.)90.000, 110.470, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a pair of beta sheets. One sheet is constructed from chain A and unit cell translations along the b direction (i.e. X,Y+1,Z; X,Y+2,Z; X,Y+3,Z, etc.). The second sheet is constructed from -1/2-X,1/2+Y,-Z; -1/2-X,3/2+Y,-Z; -1/2-X,5/2+Y,-Z; etc.).

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Components

#1: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 749.917 Da / Num. of mol.: 1 / Fragment: UNP residues 623-628 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.56 Å3/Da / Density % sol: 21.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: reservoir contained 14% iso-Propanol, 0.07M HEPES-Na pH 7.5, 0.14M Sodium Citrate, and 30% Glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. all: 825 / Num. obs: 825 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.7 / Num. unique all: 156 / % possible all: 82.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ON9

2on9


Resolution: 1.51→16.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8187 / SU B: 1.895 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0982 / SU Rfree: 0.0894 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 91 11.1 %RANDOM
Rwork0.177 ---
obs0.1791 823 92.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 26.57 Å2 / Biso mean: 7.5741 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.11 Å2
2---0.21 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.51→16.78 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms53 0 0 1 54
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0259
X-RAY DIFFRACTIONr_bond_other_d0.0010.0270
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.01481
X-RAY DIFFRACTIONr_angle_other_deg0.4423160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.38357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.771252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.0041513
X-RAY DIFFRACTIONr_chiral_restr0.0970.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0260
X-RAY DIFFRACTIONr_gen_planes_other00.0212
LS refinement shellResolution: 1.508→1.547 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 4 -
Rwork0.223 45 -
all-49 -
obs--73.13 %

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