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- PDB-4e0o: SVQIVYK segment from human Tau (305-311) displayed on 54-membered... -

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Basic information

Entry
Database: PDB / ID: 4e0o
TitleSVQIVYK segment from human Tau (305-311) displayed on 54-membered macrocycle scaffold (form III)
ComponentsCyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
KeywordsPROTEIN FIBRIL / amyloid / out-of-register / fiber-forming / macrocycle
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / negative regulation of kinase activity / regulation of long-term synaptic depression / negative regulation of tubulin deacetylation / generation of neurons / rRNA metabolic process / internal protein amino acid acetylation / regulation of chromosome organization / regulation of mitochondrial fission / axonal transport of mitochondrion / intracellular distribution of mitochondria / axon development / central nervous system neuron development / regulation of microtubule polymerization / apolipoprotein binding / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / glial cell projection / protein polymerization / axolemma / negative regulation of mitochondrial fission / regulation of microtubule polymerization or depolymerization / Caspase-mediated cleavage of cytoskeletal proteins / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / positive regulation of protein localization / cytoplasmic microtubule organization / stress granule assembly / supramolecular fiber organization / regulation of calcium-mediated signaling / axon cytoplasm / somatodendritic compartment / positive regulation of microtubule polymerization / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / nuclear periphery / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / response to lead ion / microglial cell activation / synapse organization / Hsp90 protein binding / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / : / memory / SH3 domain binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-folding chaperone binding / single-stranded DNA binding / actin binding / cellular response to heat / protein-macromolecule adaptor activity / double-stranded DNA binding / growth cone / cell body / microtubule binding / sequence-specific DNA binding / microtubule / amyloid fibril formation / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding
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
PHOSPHATE ION / Microtubule-associated protein tau
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsZhao, M. / Liu, C. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates.
Authors: Liu, C. / Zhao, M. / Jiang, L. / Cheng, P.N. / Park, J. / Sawaya, M.R. / Pensalfini, A. / Gou, D. / Berk, A.J. / Glabe, C.G. / Nowick, J. / Eisenberg, D.
History
DepositionMar 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jan 29, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_polymer_linkage / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
B: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
C: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
D: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,84014
Polymers7,7284
Non-polymers1,11210
Water90150
1
A: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
B: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4327
Polymers3,8642
Non-polymers5685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-39 kcal/mol
Surface area3210 Å2
MethodPISA
2
C: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
D: Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4097
Polymers3,8642
Non-polymers5445
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-34 kcal/mol
Surface area3290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.410, 25.430, 52.530
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)


Mass: 1932.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic molecule / References: UniProt: P10636*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Na/K phosphate buffer pH 6.2, 35% (v/v) 2-methyl-2,4-pentanediol, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.82→18.37 Å / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.25 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.33
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.90.4112.53196.2
1.9-1.950.2893.47195.3
1.95-2.010.2284.04195.9
2.01-2.070.1795.27197.4
2.07-2.140.1546.45196.3
2.14-2.210.1157.17197.3
2.21-2.290.1257.86197.2
2.29-2.390.1147.88196.9
2.39-2.490.0839.81196.3
2.49-2.620.07610.01197.8
2.62-2.760.06712.2196.6
2.76-2.930.05313.57197.8
2.93-3.130.04715.88196.5
3.13-3.380.04217.66196.1
3.38-3.70.03620.11194.8
3.7-4.140.03320.68196.2
4.14-4.780.0322.81196.2
4.78-5.850.02922.96197
5.85-8.270.02621.66196.5
8.270.02423.54188.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å18.37 Å
Translation2 Å18.37 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→18.37 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.9206 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.989 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 369 5.01 %RANDOM
Rwork0.1818 ---
obs0.1842 7365 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.9989 Å20 Å2-0.351 Å2
2---4.4835 Å20 Å2
3---2.4846 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: LAST / Resolution: 1.82→18.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 71 50 641
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01646HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.38869HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d129SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes97HARMONIC5
X-RAY DIFFRACTIONt_it430HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.82→2.04 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2168 103 5.03 %
Rwork0.1687 1945 -
all0.1712 2048 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.84920.1395-1.41444.17041.2661.9376-0.01940.1181-0.002-0.0831-0.15370.32660.158-0.16590.1731-0.02790.0009-0.0064-0.090.00080.004310.4438-1.906523.2075
22.3895-1.6697-2.71455.19722.8133.71850.18480.29650.1487-0.3851-0.18970.0221-0.1307-0.20340.0049-0.15070.0157-0.0114-0.1791-0.0059-0.050111.8818.201321.8595
30.15180.00140.7424.3502-1.45012.56460.1262-0.03090.01970.2342-0.208-0.4126-0.24110.34860.08180.06820.002-0.0025-0.05380.03670.01535.24279.6723-0.8092
4-0.01250.19430.2657.45371.01813.36830.21770.0841-0.0601-0.0967-0.1541-0.50750.15270.2822-0.06360.01350.0035-0.0343-0.08770.02420.0064.4004-0.3648-2.9006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 13
2X-RAY DIFFRACTION2B0 - 13
3X-RAY DIFFRACTION3C0 - 13
4X-RAY DIFFRACTION4D0 - 13

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