|Entry||Database: PDB / ID: 6a6b|
|Title||cryo-em structure of alpha-synuclein fiber|
|Keywords||PROTEIN FIBRIL / alpha-syn fiber / Parkinson disease|
|Function / homology||Amyloid fiber formation / Synuclein / Synuclein / Alpha-synuclein / regulation of phospholipase activity / regulation of acyl-CoA biosynthetic process / neutral lipid metabolic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of mitochondrial electron transport, NADH to ubiquinone / response to desipramine ...Amyloid fiber formation / Synuclein / Synuclein / Alpha-synuclein / regulation of phospholipase activity / regulation of acyl-CoA biosynthetic process / neutral lipid metabolic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of mitochondrial electron transport, NADH to ubiquinone / response to desipramine / negative regulation of monooxygenase activity / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / regulation of glutamate secretion / regulation of reactive oxygen species biosynthetic process / negative regulation of transporter activity / negative regulation of chaperone-mediated autophagy / regulation of locomotion / regulation of norepinephrine uptake / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / positive regulation of inositol phosphate biosynthetic process / response to iron(II) ion / positive regulation of neurotransmitter secretion / negative regulation of serotonin uptake / mitochondrial ATP synthesis coupled electron transport / dopamine biosynthetic process / negative regulation of histone acetylation / synaptic vesicle transport / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / nuclear outer membrane / positive regulation of receptor recycling / regulation of dopamine secretion / regulation of macrophage activation / dynein complex binding / negative regulation of dopamine metabolic process / positive regulation of endocytosis / beta-tubulin binding / supramolecular fiber organization / alpha-tubulin binding / phospholipase binding / kinesin binding / response to magnesium ion / response to interferon-gamma / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / cellular response to fibroblast growth factor stimulus / synaptic vesicle endocytosis / regulation of presynapse assembly / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / behavioral response to cocaine / response to interleukin-1 / excitatory postsynaptic potential / inclusion body / regulation of transmembrane transporter activity / Hsp70 protein binding / microglial cell activation / synapse organization / adult locomotory behavior / cellular response to epinephrine stimulus / phospholipid metabolic process / positive regulation of protein serine/threonine kinase activity / long-term synaptic potentiation / fatty acid metabolic process / rough endoplasmic reticulum / negative regulation of protein phosphorylation / receptor internalization / ferrous iron binding / positive regulation of release of sequestered calcium ion into cytosol / synaptic vesicle membrane / cellular response to copper ion / protein destabilization / negative regulation of neuron death / regulation of long-term neuronal synaptic plasticity / phosphoprotein binding / tau protein binding / terminal bouton / positive regulation of inflammatory response / phospholipid binding / mitochondrial intermembrane space / postsynapse / actin cytoskeleton / activation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron death / cell cortex / cellular response to oxidative stress / growth cone / actin binding / mitochondrial inner membrane / histone binding / transcription regulatory region DNA binding / positive regulation of peptidyl-serine phosphorylation / protein N-terminus binding / ribosome|
Function and homology information
|Specimen source||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.07 Å resolution|
|Authors||Li, Y.W. / Zhao, C.Y. / Luo, F. / Liu, Z. / Gui, X. / Luo, Z. / Zhang, X. / Li, D. / Liu, C. / Li, X.|
|Citation||Journal: Cell Res. / Year: 2018|
Title: Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy.
Authors: Yaowang Li / Chunyu Zhao / Feng Luo / Zhenying Liu / Xinrui Gui / Zhipu Luo / Xiang Zhang / Dan Li / Cong Liu / Xueming Li
SummaryFull reportAbout validation report
|Date||Deposition: Jun 27, 2018 / Release: Jul 11, 2018|
|Structure viewer||Molecule: |
Downloads & links
Mass: 6251.097 Da / Num. of mol.: 12 / Fragment: UNP residues 37-99 / Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P37840
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: helical reconstruction|
|Component||Name: alpha-synuclein fiber / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Escherichia coli K-12 (bacteria)|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: 4 microl of alpha-syn fibril solution was applied to a glow-discharged holey carbon grid (Quantifoil R1.2/1.3, 300 mesh), blotted for 6 s, and plunge-frozen in liquid ethane using FEI Vitrobot Mark IV. 95% humidity, 16 degrees|
Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 289|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Average exposure time: 8 / Electron dose: 50 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Image scans||Movie frames/image: 32 / Used frames/image: 1-32|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: 179.641 / Axial rise/subunit: 2.393 / Axial symmetry: C1|
|3D reconstruction||Resolution: 3.07 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43677 / Symmetry type: HELICAL|
-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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-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.
+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
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