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- PDB-3ovl: Structure of an amyloid forming peptide VQIVYK from the TAU prote... -

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Basic information

Entry
Database: PDB / ID: 3ovl
TitleStructure of an amyloid forming peptide VQIVYK from the TAU protein in complex with orange G
ComponentsMicrotubule-associated protein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril in complex with a small-molecule binder
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 / regulation of microtubule polymerization / dynactin binding / 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 / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / somatodendritic compartment / positive regulation of microtubule polymerization / axon cytoplasm / astrocyte activation / phosphatidylinositol binding / stress granule assembly / 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 / protein homooligomerization / synapse organization / regulation of synaptic plasticity / PKR-mediated signaling / response to lead ion / SH3 domain binding / 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 / microtubule cytoskeleton / growth cone / cell body / actin binding / 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 / DNA damage response / dendrite / 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
ACETIC ACID / Chem-ORA / Microtubule-associated protein tau
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsLandau, M. / Eisenberg, D.
CitationJournal: Plos Biol. / Year: 2011
Title: Towards a pharmacophore for amyloid.
Authors: Landau, M. / Sawaya, M.R. / Faull, K.F. / Laganowsky, A. / Jiang, L. / Sievers, S.A. / Liu, J. / Barrio, J.R. / Eisenberg, D.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3495
Polymers7501
Non-polymers5994
Water362
1
A: Microtubule-associated protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)8,09530
Polymers4,5006
Non-polymers3,59624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,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
Unit cell
Length a, b, c (Å)55.056, 4.831, 22.127
Angle α, β, γ (deg.)90.000, 102.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7-

ZN

DetailsThe biological unit is a pair of beta sheets with orange G interrelating between two pairs of 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 -X-1/2,1/2+Y,-Z;-X-1/2,3/2+Y,-Z;-X-1/2,5/2+Y,-Z; etc. The other pairs of sheets will be contracted from -X,Y,-Z+1, -X,Y+1,-Z+1,-X,Y+2,-Z+1; etc. and from X+1/2,1/2+Y,Z+1, X+1/2,3/2+Y,Z+1, X+1/2,5/2+Y,Z+1; etc.

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Components

#1: Protein/peptide Microtubule-associated protein


Mass: 749.917 Da / Num. of mol.: 1 / Fragment: VQIVYK (residues 306-311) / Source method: obtained synthetically / Details: VQIVYK (residues 306-311) from Tau, synthesized / References: UniProt: P10636
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-ORA / 7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid / Orange G


Mass: 408.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N2O7S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: reservoir contained 0.1M Zinc Acetate dihydrate, 18% PEG 3350, vapor diffusion, hanging drop, temperature 291K

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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: Nov 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 587 / Num. obs: 587 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.179 / Χ2: 1.071 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.941.40.433881.077171
1.94-2.131.60.2811061.081179.1
2.13-2.442.70.4751281.05190.1
2.44-3.083.10.351121.065199.1
3.08-902.90.1631531.088197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å26.82 Å
Translation1.8 Å26.82 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→26.82 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.306 / WRfactor Rwork: 0.2514 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.7697 / SU B: 5.919 / SU ML: 0.163 / SU R Cruickshank DPI: 0.3608 / SU Rfree: 0.2072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 61 10.4 %RANDOM
Rwork0.2589 ---
all0.2589 586 --
obs0.2589 586 87.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 36.92 Å2 / Biso mean: 20.2828 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.24 Å2
2---0.7 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.81→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53 0 33 2 88
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02285
X-RAY DIFFRACTIONr_bond_other_d0.0050.0244
X-RAY DIFFRACTIONr_angle_refined_deg1.222.402118
X-RAY DIFFRACTIONr_angle_other_deg0.6273104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.537252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.4411511
X-RAY DIFFRACTIONr_chiral_restr0.080.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0280
X-RAY DIFFRACTIONr_gen_planes_other00.0218
X-RAY DIFFRACTIONr_mcbond_it1.0891.533
X-RAY DIFFRACTIONr_mcbond_other0.411.511
X-RAY DIFFRACTIONr_mcangle_it1.64252
X-RAY DIFFRACTIONr_scbond_it2.252352
X-RAY DIFFRACTIONr_scangle_it3.3194.566
LS refinement shellResolution: 1.805→2.017 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.448 21 -
Rwork0.377 118 -
all-139 -
obs--76.37 %

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