[English] 日本語
Yorodumi
- PDB-2n0a: Atomic-resolution structure of alpha-synuclein fibrils -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n0a
TitleAtomic-resolution structure of alpha-synuclein fibrils
ComponentsAlpha-synuclein
KeywordsSTRUCTURAL PROTEIN / Protein Fibril / Amyloid / Parkinson's Disease
Function / homology
Function and homology information


regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / regulation of synaptic vesicle recycling / 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 / response to iron(II) ion / regulation of norepinephrine uptake / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / dopamine uptake involved in synaptic transmission / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / response to magnesium ion / response to type II interferon / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / : / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / protein destabilization / negative regulation of protein kinase activity / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / positive regulation of protein serine/threonine kinase activity / tau protein binding / PKR-mediated signaling / receptor internalization / : / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / response to lipopolysaccharide / amyloid fibril formation / molecular adaptor activity / lysosome / transcription cis-regulatory region binding / oxidoreductase activity / positive regulation of apoptotic process
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsTuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Schwieters, C.D. / Lee, V.M. ...Tuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Schwieters, C.D. / Lee, V.M. / George, J.M. / Rienstra, C.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Solid-state NMR structure of a pathogenic fibril of full-length human alpha-synuclein.
Authors: Tuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Barclay, A.M. / Kendall, A. / Wan, W. / Stubbs, G. / Schwieters, ...Authors: Tuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Barclay, A.M. / Kendall, A. / Wan, W. / Stubbs, G. / Schwieters, C.D. / Lee, V.M. / George, J.M. / Rienstra, C.M.
History
DepositionMar 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 1, 2016Group: Structure summary
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
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
G: Alpha-synuclein
H: Alpha-synuclein
I: Alpha-synuclein
J: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)144,76110
Polymers144,76110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area108397.4 Å2
ΔGint30.2 kcal/mol
Surface area53490.2 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 256structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 14476.108 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Plasmid: pET28a-AS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37840

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR
Details: Atomic-resolution structure of alpha-synuclein fibrils
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
117Cross Polarization C1D
1213D NCACX
1313D NCOCX
1413D CANCO
1512D CC DARR
1622D CC DARR
1723D NCOCX
1822D NC TEDOR
1922D CC DARR
11022D CC DARR
11123D NCOCX
11232D CC DARR
11333D NCACX
11432D CC DARR
11532D NC TEDOR
11632D CC DARR
11733D NCACX
11842D NC TEDOR
11952D NC TEDOR
12062D CC DARR
12162D ChhC

-
Sample preparation

Details
Solution-IDContentsSolvent system
166% [U-100% 13C; U-100% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
266% [U-100% 13C 1,3-Glycerol; U-100% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
366% [U-100% 13C 2-Glycerol; U-100% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
466% [U-25% 13C; U-25% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
566% [U-25% 13C 1,3-Glycerol; natural abundance N][natural abundance C13, U-50% N15] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
666% [U-25% 13C 2-Glycerol; natural abundance N][natural abundance C13, U-50% N15] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
790% Adamantane, 10% KBr, DryDry
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
66 %alpha-synuclein-1[U-100% 13C; U-100% 15N]1
34 %H2O-21
66 %alpha-synuclein-3[U-100% 13C 1,3-Glycerol; U-100% 15N]2
34 %H2O-42
66 %alpha-synuclein-5[U-100% 13C 2-Glycerol; U-100% 15N]3
34 %H2O-63
66 %alpha-synuclein-7[U-25% 13C; U-25% 15N]4
34 %H2O-84
66 %alpha-synuclein-9[U-25% 13C 1,3-Glycerol; natural abundance N][natural abundance C13, U-50% N15]5
34 %H2O-105
66 %alpha-synuclein-11[U-25% 13C 2-Glycerol; natural abundance N][natural abundance C13, U-50% N15]6
34 %H2O-126
90 %Adamantane-137
10 %KBr-147
Sample conditionspH: 7 / Pressure: ambient / Temperature units: K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent VNMRSAgilentVNMRS7501
Agilent InfinityPlusAgilentInfinityPlus6002
Agilent VNMRSAgilentVNMRS5003

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.33.4Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIH2.33.4Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.33.4Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 450 / Protein psi angle constraints total count: 450
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 256 / Conformers submitted total number: 1 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å / Representative conformer: 1 / Torsion angle constraint violation method: Degrees
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

+
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