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- PDB-6nk4: KVQIINKKL, crystal structure of a tau protein fragment -

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Basic information

Entry
Database: PDB / ID: 6nk4
TitleKVQIINKKL, crystal structure of a tau protein fragment
ComponentsMicrotubule-associated protein tau
KeywordsSTRUCTURAL PROTEIN / Amyloid / tau / Alzheimer's Disease / tauopathy / MAPT
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 / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / glial cell projection / apolipoprotein binding / 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 / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / : / memory / microtubule cytoskeleton organization / SH3 domain binding / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / microtubule cytoskeleton / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / actin binding / cellular response to heat / protein-macromolecule adaptor activity / growth cone / cell body / double-stranded DNA binding / 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 / dendrite / DNA damage response / 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
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 1.994 Å
Model detailsCrystal structure KVQIINKL from the microtubule binding region of tau protein reveals a tightly ...Crystal structure KVQIINKL from the microtubule binding region of tau protein reveals a tightly packed steric zipper
AuthorsEisenberg, D.S. / Boyer, D.R. / Sawaya, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG0543022 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines.
Authors: Catharine Shipps / H Ray Kelly / Peter J Dahl / Sophia M Yi / Dennis Vu / David Boyer / Calina Glynn / Michael R Sawaya / David Eisenberg / Victor S Batista / Nikhil S Malvankar /
Abstract: Proteins are commonly known to transfer electrons over distances limited to a few nanometers. However, many biological processes require electron transport over far longer distances. For example, ...Proteins are commonly known to transfer electrons over distances limited to a few nanometers. However, many biological processes require electron transport over far longer distances. For example, soil and sediment bacteria transport electrons, over hundreds of micrometers to even centimeters, via putative filamentous proteins rich in aromatic residues. However, measurements of true protein conductivity have been hampered by artifacts due to large contact resistances between proteins and electrodes. Using individual amyloid protein crystals with atomic-resolution structures as a model system, we perform contact-free measurements of intrinsic electronic conductivity using a four-electrode approach. We find hole transport through micrometer-long stacked tyrosines at physiologically relevant potentials. Notably, the transport rate through tyrosines (10 s) is comparable to cytochromes. Our studies therefore show that amyloid proteins can efficiently transport charges, under ordinary thermal conditions, without any need for redox-active metal cofactors, large driving force, or photosensitizers to generate a high oxidation state for charge injection. By measuring conductivity as a function of molecular length, voltage, and temperature, while eliminating the dominant contribution of contact resistances, we show that a multistep hopping mechanism (composed of multiple tunneling steps), not single-step tunneling, explains the measured conductivity. Combined experimental and computational studies reveal that proton-coupled electron transfer confers conductivity; both the energetics of the proton acceptor, a neighboring glutamine, and its proximity to tyrosine influence the hole transport rate through a proton rocking mechanism. Surprisingly, conductivity increases 200-fold upon cooling due to higher availability of the proton acceptor by increased hydrogen bonding.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 30, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 11, 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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Assembly

Deposited unit
A: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)1,0861
Polymers1,0861
Non-polymers00
Water543
1
A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau

A: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)10,86410
Polymers10,86410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_558x,y,z+31
crystal symmetry operation1_559x,y,z+41
crystal symmetry operation4_545-x,-y-1,z+1/21
crystal symmetry operation4_546-x,-y-1,z+3/21
crystal symmetry operation4_547-x,-y-1,z+5/21
crystal symmetry operation4_548-x,-y-1,z+7/21
crystal symmetry operation4_549-x,-y-1,z+9/21
Unit cell
Length a, b, c (Å)62.906, 62.906, 4.832
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 1086.390 Da / Num. of mol.: 1 / Fragment: repeat 2 peptide (UNP residues 591-599) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: KVQIINKKL Tau peptide / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
EM crystal formationInstrument: hanging drop vapor diffusion / Atmosphere: air / Details: 0.2 M lithium citrate, 20% PEG3350 / Lipid mixture: none / Temperature: 291 K
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE
CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium citrate, 20% PEG3350

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Data collection

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 0.1 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM diffractionCamera length: 1850 mm
EM diffraction shellResolution: 2→2.15 Å / Fourier space coverage: 95.7 % / Multiplicity: 4.9 / Num. of structure factors: 174 / Phase residual: 0.1 °
EM diffraction statsFourier space coverage: 97.1 % / High resolution: 2 Å / Num. of intensities measured: 943 / Num. of structure factors: 943 / Phase error: 0 ° / Phase residual: 0.1 ° / Phase error rejection criteria: 0 / Rmerge: 0.244 / Rsym: 0.244
DiffractionMean temperature: 88 K / Serial crystal experiment: N
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251 Å
DetectorType: TVIPS F416 CMOS CAMERA / Detector: CMOS / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1.994→90 Å / Num. obs: 943 / % possible obs: 97.1 % / Redundancy: 6 % / Biso Wilson estimate: 22.14 Å2 / Rmerge(I) obs: 0.244 / Χ2: 1.394 / Net I/σ(I): 2.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.154.90.6811741.038196.7
2.15-2.377.30.641961.162196.1
2.37-2.716.40.3661661.193198.8
2.71-3.425.50.3271851.362199.5
3.42-27.245.60.1442222.11195.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
EM softwareName: PHENIX / Version: 1.11.1_2575 / Category: model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 62.906 Å / B: 62.906 Å / C: 4.832 Å / Space group name: P61 / Space group num: 169
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5V5B

5v5b


Resolution: 1.994→27.24 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.1
RfactorNum. reflection% reflection
Rfree0.2991 84 8.99 %
Rwork0.2601 --
obs0.2638 934 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.32 Å2 / Biso mean: 18.6573 Å2 / Biso min: 3.33 Å2
Refinement stepCycle: final / Resolution: 1.994→54.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76 0 0 3 79
Biso mean---17.98 -
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0175
ELECTRON CRYSTALLOGRAPHYf_angle_d1.39998
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.11413
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00511
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d17.50333
LS refinement shellResolution: 1.9944→27.24 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2991 84 -
Rwork0.2601 850 -
obs--96 %

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