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- PDB-9b3c: type 2 KD-mxyl filament of miniature tau macrocycle derived from ... -

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Basic information

Entry
Database: PDB / ID: 9b3c
Titletype 2 KD-mxyl filament of miniature tau macrocycle derived from 4R tauopathic fold
Components
  • GLY-SER-VAL-GLN-ILE-VAL-TYR
  • Microtubule-associated protein tau
KeywordsPROTEIN FIBRIL / tauopathies / neurodegenerative disorders / seed-competent miniature tau macrocycle
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 / dynactin binding / regulation of microtubule polymerization / 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 / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / 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 / cell body / growth cone / 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 / negative regulation of gene expression / axon / 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
1,3-dimethylbenzene / AMINO GROUP / Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsXu, X. / Angera, J.I. / Rajewski, H.B. / Jiang, W. / Del Valle, R.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG074570 United States
National Science Foundation (NSF, United States)CHE2109008 United States
CitationJournal: To Be Published
Title: Structure-based design of seed-competent proteomimetic macrocycles derived from 4R tauopathic folds
Authors: Xu, X. / Angera, J.I. / Rajewski, H.B. / Jiang, W. / Del Valle, R.J.
History
DepositionMar 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated protein tau
G: Microtubule-associated protein tau
M: Microtubule-associated protein tau
S: Microtubule-associated protein tau
B: GLY-SER-VAL-GLN-ILE-VAL-TYR
H: GLY-SER-VAL-GLN-ILE-VAL-TYR
N: GLY-SER-VAL-GLN-ILE-VAL-TYR
T: GLY-SER-VAL-GLN-ILE-VAL-TYR
C: Microtubule-associated protein tau
I: Microtubule-associated protein tau
O: Microtubule-associated protein tau
U: Microtubule-associated protein tau
D: GLY-SER-VAL-GLN-ILE-VAL-TYR
J: GLY-SER-VAL-GLN-ILE-VAL-TYR
P: GLY-SER-VAL-GLN-ILE-VAL-TYR
V: GLY-SER-VAL-GLN-ILE-VAL-TYR
E: Microtubule-associated protein tau
K: Microtubule-associated protein tau
Q: Microtubule-associated protein tau
W: Microtubule-associated protein tau
F: GLY-SER-VAL-GLN-ILE-VAL-TYR
L: GLY-SER-VAL-GLN-ILE-VAL-TYR
R: GLY-SER-VAL-GLN-ILE-VAL-TYR
X: GLY-SER-VAL-GLN-ILE-VAL-TYR
Y: Microtubule-associated protein tau
Z: GLY-SER-VAL-GLN-ILE-VAL-TYR
a: Microtubule-associated protein tau
b: GLY-SER-VAL-GLN-ILE-VAL-TYR
c: Microtubule-associated protein tau
d: GLY-SER-VAL-GLN-ILE-VAL-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94560
Polymers45,11330
Non-polymers1,83330
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 2242.640 Da / Num. of mol.: 15 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#2: Protein/peptide
GLY-SER-VAL-GLN-ILE-VAL-TYR


Mass: 764.867 Da / Num. of mol.: 15 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: NH2
#4: Chemical
ChemComp-8VH / 1,3-dimethylbenzene


Mass: 106.165 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C8H10
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: type 2 KD-mxyl filament of miniature tau macrocycle derived from 4R tauopathic fold
Type: CELL / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 59.495 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.2 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27196 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0083300
ELECTRON MICROSCOPYf_angle_d0.6564440
ELECTRON MICROSCOPYf_dihedral_angle_d8.375450
ELECTRON MICROSCOPYf_chiral_restr0.068495
ELECTRON MICROSCOPYf_plane_restr0.007555

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