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- PDB-5k7n: MicroED structure of tau VQIVYK peptide at 1.1 A resolution -

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Basic information

Entry
Database: PDB / ID: 5k7n
TitleMicroED structure of tau VQIVYK peptide at 1.1 A resolution
ComponentsVQIVYK
KeywordsPROTEIN FIBRIL / Amyloid
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 / regulation of chromosome organization / positive regulation of protein localization / 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 / cellular response to reactive oxygen species / SH3 domain binding / microtubule cytoskeleton organization / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / cellular response to heat / 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
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.1 Å
Authorsde la Cruz, M.J. / Hattne, J. / Shi, D. / Seidler, P. / Rodriguez, J. / Reyes, F.E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Gonen, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R01-AG029430 United States
CitationJournal: Nat Methods / Year: 2017
Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen /
Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
Z: VQIVYK


Theoretical massNumber of molelcules
Total (without water)7501
Polymers7501
Non-polymers00
Water362
1
Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK


Theoretical massNumber of molelcules
Total (without water)6,7499
Polymers6,7499
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
Unit cell
Length a, b, c (Å)29.420, 4.990, 37.170
Angle α, β, γ (deg.)90.00, 111.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11Z-102-

HOH

DetailsThe biological unit is an extended pair of beta sheets comprising peptides at position X,Y,Z extended ad infinitum along the b crystal axis.

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Components

#1: Protein/peptide VQIVYK / tau peptide


Mass: 749.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#2: 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: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: VQIVYK / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.000747 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8.5
Buffer component
IDConc.NameBuffer-ID
122.5 %ethylene glycol1
2Tris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Apr 26, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.1 sec. / Electron dose: 0.002 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 299 / Num. of grids imaged: 1 / Num. of real images: 299
Image scansSampling size: 0.0311999992 µm / Width: 2048 / Height: 2048
EM diffractionCamera length: 730 mm
EM diffraction shellResolution: 1.1→1.23 Å / Fourier space coverage: 79.4 % / Multiplicity: 1.8 / Num. of structure factors: 255 / Phase residual: 47.6 °
EM diffraction statsFourier space coverage: 83 % / High resolution: 1.1 Å / Num. of intensities measured: 6185 / Num. of structure factors: 3319 / Phase error: 0 ° / Phase residual: 39.4 ° / Phase error rejection criteria: 0 / Rmerge: 12.9 / Rsym: 12.9
ReflectionResolution: 1.1→14.7 Å / Num. all: 6185 / Num. obs: 3319 / % possible obs: 83 % / Redundancy: 1.9 % / Biso Wilson estimate: 8.35 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 2.4
Reflection shellResolution: 1.1→1.23 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.472 / Num. unique all: 463 / Num. unique obs: 255 / Rsym value: 0.472 / Net I/σ(I) obs: 1.1 / % possible all: 79.4

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EM-Menu4.0.9.75image acquisition
5XDSMay 1, 2016diffraction indexing
7SHELXT2014/5otherphasing
11XDSMay 1, 2016crystallography merging
13BUSTER2.10.0model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 111.55 ° / ∠γ: 90 ° / A: 29.42 Å / B: 4.99 Å / C: 37.17 Å / Space group name: C121 / Space group num: 5
CTF correctionType: NONE
3D reconstructionResolution: 1.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
RefinementResolution: 1.1→14.7 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9516 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.046 / SU Rfree Blow DPI: 0.046 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 190 10.01 %RANDOM
Rwork0.2097 ---
obs0.211 1898 81.11 %-
Displacement parametersBiso mean: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.6602 Å20 Å23.1898 Å2
2--0.0678 Å20 Å2
3----1.728 Å2
Refine analyzeLuzzati coordinate error obs: 0.203 Å
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
ELECTRON CRYSTALLOGRAPHYt_bond_d0.012111HARMONIC2
ELECTRON CRYSTALLOGRAPHYt_angle_deg0.77202HARMONIC2
ELECTRON CRYSTALLOGRAPHYt_dihedral_angle_d26SINUSOIDAL2
ELECTRON CRYSTALLOGRAPHYt_incorr_chiral_ct
ELECTRON CRYSTALLOGRAPHYt_pseud_angle
ELECTRON CRYSTALLOGRAPHYt_trig_c_planes2HARMONIC2
ELECTRON CRYSTALLOGRAPHYt_gen_planes12HARMONIC5
ELECTRON CRYSTALLOGRAPHYt_it111HARMONIC20
ELECTRON CRYSTALLOGRAPHYt_nbd0SEMIHARMONIC5
ELECTRON CRYSTALLOGRAPHYt_omega_torsion1.62
ELECTRON CRYSTALLOGRAPHYt_other_torsion9.65
ELECTRON CRYSTALLOGRAPHYt_improper_torsion
ELECTRON CRYSTALLOGRAPHYt_chiral_improper_torsion7SEMIHARMONIC5
ELECTRON CRYSTALLOGRAPHYt_sum_occupancies
ELECTRON CRYSTALLOGRAPHYt_utility_distance
ELECTRON CRYSTALLOGRAPHYt_utility_angle
ELECTRON CRYSTALLOGRAPHYt_utility_torsion
ELECTRON CRYSTALLOGRAPHYt_ideal_dist_contact68SEMIHARMONIC4
LS refinement shellResolution: 1.1→1.23 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2243 54 9.94 %
Rwork0.2104 489 -
all0.2117 543 -
obs--81.11 %
Refinement TLS params.Method: refined / Origin x: 10.8417 Å / Origin y: 1.956 Å / Origin z: 8.5763 Å
111213212223313233
T-0.0041 Å2-0.0004 Å20.0615 Å2--0.0667 Å2-0.0046 Å2--0.0721 Å2
L0.4341 °20.2835 °20.124 °2-0.6654 °20.2447 °2--0.0381 °2
S-0.0138 Å °0.0028 Å °0.002 Å °-0.0426 Å °0.0046 Å °0.0052 Å °0.028 Å °0.0029 Å °0.0092 Å °
Refinement TLS groupSelection details: { Z|* }

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