[English] 日本語
- PDB-6flt: Structure of alpha-synuclein fibrils -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6flt
TitleStructure of alpha-synuclein fibrils
KeywordsPROTEIN FIBRIL / Parkinson's disease / apha-synuclein / fibril / filament
Function / homologyAmyloid fiber formation / Synuclein / Alpha-synuclein / Synuclein / negative regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of norepinephrine uptake / neutral lipid metabolic process / response to desipramine / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of monooxygenase activity ...Amyloid fiber formation / Synuclein / Alpha-synuclein / Synuclein / negative regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of norepinephrine uptake / neutral lipid metabolic process / response to desipramine / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of monooxygenase activity / regulation of phospholipase activity / positive regulation of glutathione peroxidase activity / regulation of acyl-CoA biosynthetic process / positive regulation of hydrogen peroxide catabolic process / mitochondrial membrane organization / supramolecular fiber / regulation of glutamate secretion / regulation of reactive oxygen species biosynthetic process / negative regulation of transporter activity / regulation of presynapse assembly / negative regulation of chaperone-mediated autophagy / regulation of norepinephrine uptake / regulation of locomotion / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of inositol phosphate biosynthetic process / negative regulation of exocytosis / response to iron(II) ion / positive regulation of neurotransmitter secretion / negative regulation of serotonin uptake / dopamine biosynthetic process / mitochondrial ATP synthesis coupled electron transport / negative regulation of histone acetylation / synaptic vesicle transport / positive regulation of receptor recycling / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / nuclear outer membrane / synaptic vesicle endocytosis / regulation of macrophage activation / negative regulation of dopamine metabolic process / dynein complex binding / beta-tubulin binding / supramolecular fiber organization / alpha-tubulin binding / phospholipase binding / positive regulation of endocytosis / kinesin binding / response to magnesium ion / cellular response to copper ion / response to interferon-gamma / negative regulation of thrombin-activated receptor signaling pathway / cellular response to fibroblast growth factor stimulus / cuprous ion binding / excitatory postsynaptic potential / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to interleukin-1 / behavioral response to cocaine / microglial cell activation / inclusion body / long-term synaptic potentiation / fatty acid metabolic process / regulation of transmembrane transporter activity / Hsp70 protein binding / synapse organization / adult locomotory behavior / phospholipid metabolic process / cellular response to epinephrine stimulus / postsynapse / tau protein binding / synaptic vesicle / ferrous iron binding / positive regulation of protein serine/threonine kinase activity / rough endoplasmic reticulum / negative regulation of protein phosphorylation / regulation of long-term neuronal synaptic plasticity / receptor internalization / positive regulation of release of sequestered calcium ion into cytosol / terminal bouton / protein destabilization / negative regulation of neuron death / phospholipid binding / cytoplasmic vesicle membrane / positive regulation of inflammatory response / phosphoprotein binding / mitochondrial intermembrane space / actin cytoskeleton / activation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell cortex / positive regulation of neuron death / growth cone / cellular response to oxidative stress / mitochondrial inner membrane / actin binding / histone binding / transcription regulatory region DNA binding / lysosome / ribosome
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.42 Å resolution
AuthorsGuerrero-Ferreira, R. / Taylor, N.M.I. / Mona, D. / Riek, R. / Britschgi, M. / Stahlberg, H.
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of alpha-synuclein fibrils.
Authors: Ricardo Guerrero-Ferreira / Nicholas Mi Taylor / Daniel Mona / Philippe Ringler / Matthias E Lauer / Roland Riek / Markus Britschgi / Henning Stahlberg
Abstract: Parkinson's disease is a progressive neuropathological disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concentrations in ...Parkinson's disease is a progressive neuropathological disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concentrations in affected neurons. Its hallmark are intracellular inclusions called Lewy bodies and Lewy neurites. We here report the structure of cytotoxic alpha-synuclein fibrils (residues 1-121), determined by cryo-electron microscopy at a resolution of 3.4 Å. Two protofilaments form a polar fibril composed of staggered β-strands. The backbone of residues 38 to 95, including the fibril core and the non-amyloid component region, are well resolved in the EM map. Residues 50-57, containing three of the mutation sites associated with familial synucleinopathies, form the interface between the two protofilaments and contribute to fibril stability. A hydrophobic cleft at one end of the fibril may have implications for fibril elongation, and invites for the design of molecules for diagnosis and treatment of synucleinopathies.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2018 / Release: Jun 27, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 27, 2018Structure modelrepositoryInitial release
1.1Jul 11, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _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

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4276
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4276
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Alpha-synuclein
B: Alpha-synuclein
C: Alpha-synuclein
D: Alpha-synuclein
E: Alpha-synuclein
F: Alpha-synuclein
G: Alpha-synuclein
H: Alpha-synuclein
I: Alpha-synuclein
J: Alpha-synuclein

Theoretical massNumber of molelcules
Total (without water)122,42910

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)37460
ΔGint (kcal/M)-133
Surface area (Å2)21870


#1: Protein/peptide
Alpha-synuclein / / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP

Mass: 12242.873 Da / Num. of mol.: 10 / Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Plasmid name: pET21
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37840

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

Sample preparation

ComponentName: Alpha-synuclein fibrils / Type: COMPLEX / Details: Residues 1-121 / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pET21
Buffer solutionpH: 7.3
Buffer component
IDConc.NameFormulaBuffer ID
12.66 mMPotassium chlorideKCl1
21.47 mMPotassium phosphateKH2PO41
3137.93 mMSodium chlorideNaCl1
48.06 mMSodium phosphateNa2HPO41
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 50 / Used frames/image: 2-50


SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
Helical symmertyAngular rotation/subunit: -179.5 deg. / Axial rise/subunit: 2.45 Å / Axial symmetry: C1
Particle selectionDetails: Segments extracted from 792 manually picked fibrils
Number of particles selected: 18860
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13390 / Symmetry type: POINT

About Yorodumi


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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


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.

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