[English] 日本語
Yorodumi
- PDB-9rzf: Structure of in-vivo formed alpha-synuclein fibrils purified from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rzf
TitleStructure of in-vivo formed alpha-synuclein fibrils purified from a M83+/- mouse brain injected with recombinant 1B fibrils
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / Alpha-synuclein / Prion-like / Fibril / Paired helical filament
Function / homology
Function and homology information


PKR-mediated signaling / regulation of neurotransmitter secretion / platelet alpha granule membrane / membrane organization / synaptic transmission, dopaminergic / neurotransmitter secretion / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake ...PKR-mediated signaling / regulation of neurotransmitter secretion / platelet alpha granule membrane / membrane organization / synaptic transmission, dopaminergic / neurotransmitter secretion / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / arachidonate binding / SNARE complex assembly / regulation of reactive oxygen species metabolic process / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / response to iron(II) ion / positive regulation of inositol phosphate biosynthetic process / regulation of locomotion / negative regulation of dopamine metabolic process / regulation of macrophage activation / synaptic vesicle priming / transporter regulator activity / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / mitochondrial ATP synthesis coupled electron transport / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / dopamine metabolic process / cuprous ion binding / protein complex oligomerization / nuclear outer membrane / positive regulation of exocytosis / response to magnesium ion / positive regulation of endocytosis / kinesin binding / synaptic vesicle endocytosis / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / regulation of neuronal synaptic plasticity / regulation of presynapse assembly / response to type II interferon / alpha-tubulin binding / positive regulation of synaptic transmission / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / cellular response to copper ion / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / axon terminus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / excitatory postsynaptic potential / phosphoprotein binding / protein tetramerization / fatty acid metabolic process / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / actin cytoskeleton / actin binding / growth cone / cellular response to oxidative stress / cell cortex / neuron apoptotic process / response to lipopolysaccharide / microtubule binding / chemical synaptic transmission / histone binding / negative regulation of neuron apoptotic process / mitochondrial outer membrane / cytoskeleton / oxidoreductase activity / postsynapse
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
Authorsvan den Heuvel, L. / Burger, D. / Kashyrina, M. / de La Seigliere, H. / Lewis, A.J. / De Nuccio, F. / Mohammed, I. / Verchere, J. / Feuillie, C. / Berbon, M. ...van den Heuvel, L. / Burger, D. / Kashyrina, M. / de La Seigliere, H. / Lewis, A.J. / De Nuccio, F. / Mohammed, I. / Verchere, J. / Feuillie, C. / Berbon, M. / Arotcarena, M. / Retailleau, A. / Bezard, E. / Canron, M. / Meissner, W.G. / Loquet, A. / Bousset, L. / Poujol, C. / Nilsson, K.P.R. / Laferriere, F. / Baron, T. / Lofrumento, D.D. / De Giorgi, F. / Stahlberg, H. / Ichas, F.
Funding support Switzerland, France, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationIC00I0L-231578 Switzerland
Agence Nationale de la Recherche (ANR)ANR-24-CE93-0003 France
CitationJournal: To Be Published / Year: 2024
Title: Synthetic alpha-synuclein fibrils replicate in mice causing MSA neuropathology
Authors: Burger, D. / Kashyrina, M. / van den Heuvel, L. / de La Seigliere, H. / Lewis, A.J. / De Nuccio, F. / Mohammed, I. / Verchere, J. / Feuillie, C. / Berbon, M. / Arotcarena, M. / Retailleau, A. ...Authors: Burger, D. / Kashyrina, M. / van den Heuvel, L. / de La Seigliere, H. / Lewis, A.J. / De Nuccio, F. / Mohammed, I. / Verchere, J. / Feuillie, C. / Berbon, M. / Arotcarena, M. / Retailleau, A. / Bezard, E. / Canron, M. / Meissner, W.G. / Loquet, A. / Bousset, L. / Poujol, C. / Nilsson, K.P.R. / Laferriere, F. / Baron, T. / Lofrumento, D.D. / De Giorgi, F. / Stahlberg, H. / Ichas, F.
History
DepositionJul 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-synuclein
B: Alpha-synuclein
C: Alpha-synuclein
D: Alpha-synuclein
E: Alpha-synuclein
F: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)36,2276
Polymers36,2276
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
Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 6037.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: A53T / Source: (natural) Mus musculus (house mouse) / Organ: Brain / Strain: Hemizygous A53T alpha-synuclein transgenic line M83 / References: UniProt: O55042
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Alpha-synuclein fibril purified from the brain of a 1B-injected M83+/- mouse
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 14 kDa/nm / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: Hemizygous A53T alpha-synuclein transgenic line M83 / Organ: Brain
Buffer solutionpH: 7.4 / Details: 50 mM Tris-HCl, 150 mM NaCl, pH7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTris-HClTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sarkosyl-insoluble fraction
Specimen supportDetails: The grids were not glow-discharged / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 293 K

-
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 magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.04 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 42812
Details: Images were collected in movie-mode with a total of 936 frames per movie.
EM imaging opticsEnergyfilter name: TFS Selectris X
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategoryDetails
1RELION4.0.0particle selectionUsed for manual picking and helical reconstruction
2cryoSPARC4.7.0particle selectionUsed for selection of micrographs
3EPUimage acquisition
5CTFFIND4.1CTF correction
8Coot0.9.8.96model fitting
9UCSF ChimeraX1.6model fitting
14RELION4.0.03D reconstruction
15PHENIX1.21.2model refinement
Image processingDetails: A total of 40 movies was selected for manual picking
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.55 ° / Axial rise/subunit: 2.4 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 3556
Details: Particles selected by manual picking of fibril start and end points
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1913 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: A rigid-body fit was done using ChimeraX and a subsequent jiggle fit and all-atom refinement was done in Coot.
Atomic model building

3D fitting-ID: 1 / Accession code: 9EUU / Initial refinement model-ID: 1 / PDB-ID: 9EUU

9euu

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1AA
2BB
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044350
ELECTRON MICROSCOPYf_angle_d0.7665890
ELECTRON MICROSCOPYf_dihedral_angle_d5.866630
ELECTRON MICROSCOPYf_chiral_restr0.054790
ELECTRON MICROSCOPYf_plane_restr0.004720

+
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