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- PDB-4e0m: SVQIVYK segment from human Tau (305-311) displayed on 54-membered... -

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Basic information

Entry
Database: PDB / ID: 4e0m
TitleSVQIVYK segment from human Tau (305-311) displayed on 54-membered macrocycle scaffold (form I)
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 / 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 / positive regulation of protein localization / regulation of chromosome organization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / 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 / lipoprotein particle binding / dynactin binding / apolipoprotein binding / glial cell projection / negative regulation of mitochondrial membrane potential / 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 / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / regulation of cellular response to heat / stress granule assembly / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / 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 / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / SH3 domain binding / microtubule cytoskeleton organization / cellular response to reactive oxygen species / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / cellular response to heat / single-stranded DNA binding / protein-folding chaperone binding / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / 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, 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
PHOSPHATE ION / Microtubule-associated protein tau
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsZhao, M. / Liu, C. / Michael, S.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 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Advisory / Data collection / Category: pdbx_validate_polymer_linkage / reflns_shell / Item: _reflns_shell.percent_possible_all
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.pdbx_leaving_atom_flag / _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)8,62913
Polymers7,7284
Non-polymers9019
Water50428
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)4,1495
Polymers3,8642
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-2 kcal/mol
Surface area2830 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)4,4808
Polymers3,8642
Non-polymers6166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4 kcal/mol
Surface area2850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.320, 25.340, 50.780
Angle α, β, γ (deg.)90.00, 122.19, 90.00
Int Tables number5
Space group name H-MC121

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
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: 0.91609 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91609 Å / Relative weight: 1
ReflectionResolution: 1.75→18.22 Å / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.82 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.83
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.80.4242.5198.7
1.8-1.840.4142.55198.8
1.84-1.90.2863.52199.7
1.9-1.960.2254.23199.3
1.96-2.020.1624.99199.5
2.02-2.090.1386.15199.4
2.09-2.170.1257.11199.5
2.17-2.260.1327.12199.3
2.26-2.360.1187.841100
2.36-2.480.1088.02198.4
2.48-2.610.1098.8199.8
2.61-2.770.08310.4199.3
2.77-2.960.08510.77199.5
2.96-3.20.06812.43198.4
3.2-3.50.05814.111100
3.5-3.910.05815.04198.6
3.91-4.520.05615.53197.3
4.52-5.530.04116.41197.2
5.53-7.830.05215.66195
7.830.04414.97189.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→18.22 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9272 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.937 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 642 9.85 %RANDOM
Rwork0.1854 ---
obs0.1889 6519 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.8619 Å20 Å2-3.8144 Å2
2--1.8581 Å20 Å2
3---1.0038 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.75→18.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 51 28 591
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01579HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.29703HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d163SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes6HARMONIC2
X-RAY DIFFRACTIONt_gen_planes55HARMONIC5
X-RAY DIFFRACTIONt_it579HARMONIC20
X-RAY DIFFRACTIONt_nbd
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: 1.75→1.96 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2276 182 9.9 %
Rwork0.1539 1657 -
all0.1611 1839 -
obs--99.86 %
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)
10.07531.62711.27041.7450.31631.83550.04470.05580.16070.147-0.00870.14120.0567-0.004-0.0360.0110.0130.0192-0.0115-0.0117-0.0023-19.8576-27.2394-1.3919
20.9242-1.2270.04467.28242.63511.78750.1101-0.01070.0987-0.1211-0.11040.0506-0.1906-0.11360.0003-0.050.01370.0318-0.0595-0.0119-0.0751-19.1998-17.7555-3.2241
31.71490.5130.34753.69020.61352.12470.0978-0.14820.14720.0222-0.1152-0.0704-0.00210.22620.0175-0.1457-0.01070.0268-0.11380.0154-0.09061.9368-16.6877-16.4196
41.391-0.1185-0.18874.53540.27541.469-0.0514-0.2411-0.007-0.0603-0.0392-0.14220.22870.07040.0906-0.0646-0.00380.0284-0.030.015-0.05822.8193-26.4748-17.7993
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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