[English] 日本語
Yorodumi
- PDB-12aq: Cryo-EM structure of alpha-synuclein filaments (doublet) from Par... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 12aq
TitleCryo-EM structure of alpha-synuclein filaments (doublet) from Parkinson's disease with A53T mutation in SNCA
Components
  • Alpha-synuclein
  • island B
KeywordsPROTEIN FIBRIL / alpha-synuclein
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / response to desipramine / 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 chaperone-mediated autophagy / regulation of synaptic vesicle recycling / regulation of reactive oxygen species biosynthetic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / response to desipramine / 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 chaperone-mediated autophagy / regulation of synaptic vesicle recycling / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / dopamine biosynthetic process / dopamine uptake involved in synaptic transmission / negative regulation of dopamine metabolic process / response to iron(II) ion / negative regulation of platelet-derived growth factor receptor signaling pathway / SNARE complex assembly / negative regulation of microtubule polymerization / negative regulation of thrombin-activated receptor signaling pathway / synaptic vesicle priming / Lewy body / synaptic vesicle transport / regulation of norepinephrine uptake / synaptic vesicle exocytosis / transporter regulator activity / protein kinase inhibitor activity / positive regulation of inositol phosphate biosynthetic process / positive regulation of receptor recycling / cuprous ion binding / positive regulation of exocytosis / nuclear outer membrane / dynein complex binding / synaptic transmission, dopaminergic / regulation of dopamine secretion / positive regulation of endocytosis / response to magnesium ion / negative regulation of serotonin uptake / kinesin binding / cysteine-type endopeptidase inhibitor activity / regulation of presynapse assembly / synaptic vesicle endocytosis / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / cellular response to fibroblast growth factor stimulus / supramolecular fiber organization / response to type II interferon / cellular response to epinephrine stimulus / inclusion body / response to interleukin-1 / Hsp70 protein binding / axon terminus / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / enzyme inhibitor activity / glutathione metabolic process / SNARE binding / protein tetramerization / regulation of microtubule cytoskeleton organization / phosphoprotein binding / receptor internalization / protein destabilization / microglial cell activation / tubulin binding / ferrous iron binding / protein sequestering activity / phospholipid binding / synapse organization / PKR-mediated signaling / tau protein binding / enzyme activator activity / positive regulation of inflammatory response / actin cytoskeleton / terminal bouton / synaptic vesicle membrane / negative regulation of neuron apoptotic process / histone binding / actin binding / response to lipopolysaccharide / growth cone / cellular response to oxidative stress / cell cortex / oxidoreductase activity / microtubule binding / amyloid fibril formation / mitochondrial outer membrane / lysosome / transcription cis-regulatory region binding / mitochondrial inner membrane / positive regulation of apoptotic process / ribosome / mitochondrial matrix / Amyloid fiber formation / copper ion binding / protein domain specific binding / axon / lipid binding / neuronal cell body
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsZhang, H. / Yang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM structure of alpha-synuclein filaments (doublet) from Parkinson's disease with A53T mutation in SNCA
Authors: Zhang, H. / Yang, Y.
History
DepositionMar 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
J: Alpha-synuclein
K: island B


Theoretical massNumber of molelcules
Total (without water)15,2902
Polymers15,2902
Non-polymers00
Water1267
1
J: Alpha-synuclein
K: island B
x 26


Theoretical massNumber of molelcules
Total (without water)397,54252
Polymers397,54252
Non-polymers00
Water93752
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation25
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.999996, -0.002653), (0.002653, 0.999996), (1)0.3107, -0.3099, -4.78
3generate(-0.999999, 0.001326), (-0.001326, -0.999999), (1)233.7648, 234.075, -2.39
4generate(-0.999999, -0.001326), (0.001326, -0.999999), (1)234.075, 233.7648, 2.39
5generate(0.999996, 0.002653), (-0.002653, 0.999996), (1)-0.3099, 0.3107, 4.78
6generate(0.999986, 0.005306), (-0.005306, 0.999986), (1)-0.6189, 0.6222, 9.56

-
Components

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


Mass: 14506.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37840
#2: Protein/peptide island B


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of alpha-synuclein filaments (doublet) from Parkinson's disease with A53T mutation in SNCA
Type: TISSUE / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION5.1particle selection
2REFMAC5.8.0430model refinement
13Servalcat3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 179.924 ° / Axial rise/subunit: 2.39 Å / Axial symmetry: C1
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180726 / Symmetry type: HELICAL
RefinementResolution: 2.1→130.12 Å / Cor.coef. Fo:Fc: 0.666 / SU B: 6.409 / SU ML: 0.162 / ESU R: 0.085
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.5793 --
obs0.5793 115071 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 64.549 Å2
Refinement stepCycle: 1 / Total: 547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.012536
ELECTRON MICROSCOPYr_bond_other_d00.016553
ELECTRON MICROSCOPYr_angle_refined_deg0.831.806723
ELECTRON MICROSCOPYr_angle_other_deg0.3361.7491270
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.294577
ELECTRON MICROSCOPYr_dihedral_angle_2_deg
ELECTRON MICROSCOPYr_dihedral_angle_3_deg6.2551089
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0280.295
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.02608
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0296
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.1946.233314
ELECTRON MICROSCOPYr_mcbond_other3.1936.232314
ELECTRON MICROSCOPYr_mcangle_it5.33111.129389
ELECTRON MICROSCOPYr_mcangle_other5.32511.146390
ELECTRON MICROSCOPYr_scbond_it2.5436.7222
ELECTRON MICROSCOPYr_scbond_other2.5376.72223
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.44312.127335
ELECTRON MICROSCOPYr_long_range_B_refined9.01857523
ELECTRON MICROSCOPYr_long_range_B_other7.89856.41513
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.808 8484 -
obs--100 %

+
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