[English] 日本語
Yorodumi
- PDB-29os: AD fold in mouse injected with seeds of AD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29os
TitleAD fold in mouse injected with seeds of AD
ComponentsIsoform Tau-A of Microtubule-associated protein tau
KeywordsSTRUCTURAL PROTEIN / Amyloid / prion / tau / Alzheimer's Disease.
Function / homology
Function and homology information


negative regulation of tubulin deacetylation / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of intracellular transport / positive regulation of long-term synaptic depression / PKR-mediated signaling / axon extension / adult walking behavior / intrinsic apoptotic signaling pathway in response to oxidative stress / axo-dendritic transport / mitochondrion transport along microtubule ...negative regulation of tubulin deacetylation / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of intracellular transport / positive regulation of long-term synaptic depression / PKR-mediated signaling / axon extension / adult walking behavior / intrinsic apoptotic signaling pathway in response to oxidative stress / axo-dendritic transport / mitochondrion transport along microtubule / negative regulation of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / tubulin complex / positive regulation of protein localization to synapse / regulation of microtubule-based movement / intracellular distribution of mitochondria / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / apolipoprotein binding / protein polymerization / main axon / glial cell projection / mRNA transport / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / axoneme / axolemma / positive regulation of axon extension / axonal growth cone / regulation of cellular response to heat / positive regulation of microtubule polymerization / positive regulation of protein localization / axonogenesis / positive regulation of superoxide anion generation / regulation of calcium-mediated signaling / heat shock protein binding / response to nutrient / supramolecular fiber organization / somatodendritic compartment / synapse assembly / nuclear periphery / protein phosphatase 2A binding / enzyme inhibitor activity / regulation of autophagy / regulation of microtubule cytoskeleton organization / positive regulation of neuron projection development / neuron migration / Hsp90 protein binding / memory / SH3 domain binding / synapse organization / protein homooligomerization / microtubule cytoskeleton organization / response to lead ion / neuron projection development / cytoplasmic side of plasma membrane / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / growth cone / protein-folding chaperone binding / cell body / microtubule binding / amyloid fibril formation / microtubule / learning or memory / postsynaptic density / neuron projection / membrane raft / negative regulation of gene expression / axon / neuronal cell body / DNA damage response / dendrite / protein kinase binding / protein-containing complex binding / enzyme binding / DNA binding / extracellular region / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLovestam, S.L. / Scheres, S.H.W. / Goedert, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Prion-like transmission of human tau strains in the mouse brain
Authors: Lovestam, S. / Scheres, S.H.W. / Goeder, M. / Hasegawa, M.
History
DepositionMar 27, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform Tau-A of Microtubule-associated protein tau
B: Isoform Tau-A of Microtubule-associated protein tau
C: Isoform Tau-A of Microtubule-associated protein tau
D: Isoform Tau-A of Microtubule-associated protein tau
E: Isoform Tau-A of Microtubule-associated protein tau
F: Isoform Tau-A of Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)269,7716
Polymers269,7716
Non-polymers00
Water00
1


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

-
Components

#1: Protein
Isoform Tau-A of Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 44961.766 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P10637
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tau filament with the AD fold from mouse seeded by human AD tau seeds
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus (mice)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION5.1particle selection
13RELION5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.446 ° / Axial rise/subunit: 2.42 Å / Axial symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90623 / Symmetry type: HELICAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more