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- PDB-9ptb: Alpha-synuclein acetylated lysine 80 B -

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Basic information

Entry
Database: PDB / ID: 9ptb
TitleAlpha-synuclein acetylated lysine 80 B
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / acetylation / PTM
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / 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 / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / 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 / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / 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 thrombin-activated receptor signaling pathway / Lewy body / negative regulation of microtubule polymerization / synaptic vesicle priming / synaptic vesicle transport / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of inositol phosphate biosynthetic process / protein kinase inhibitor activity / regulation of dopamine secretion / positive regulation of receptor recycling / cuprous ion binding / positive regulation of exocytosis / nuclear outer membrane / dynein complex binding / synaptic transmission, dopaminergic / synaptic vesicle exocytosis / response to magnesium ion / positive regulation of endocytosis / 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 / positive regulation of release of sequestered calcium ion into cytosol / cellular response to copper ion / axon terminus / enzyme inhibitor activity / glutathione metabolic process / regulation of microtubule cytoskeleton organization / SNARE binding / protein tetramerization / protein sequestering activity / receptor internalization / phosphoprotein binding / microglial cell activation / tubulin binding / protein destabilization / ferrous iron binding / synapse organization / phospholipid binding / PKR-mediated signaling / tau protein binding / enzyme activator activity / positive regulation of inflammatory response / terminal bouton / actin cytoskeleton / synaptic vesicle membrane / growth cone / response to lipopolysaccharide / cellular response to oxidative stress / actin binding / histone binding / cell cortex / negative regulation of neuron apoptotic process / microtubule binding / amyloid fibril formation / mitochondrial outer membrane / lysosome / oxidoreductase activity / mitochondrial inner membrane / transcription cis-regulatory region binding / positive regulation of apoptotic process / ribosome / mitochondrial matrix / Amyloid fiber formation / copper ion binding / protein domain specific binding / axon / neuronal cell body / calcium ion binding
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLi, M.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RF1 NS125770 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136686 United States
CitationJournal: To Be Published
Title: Investigation of All Disease-Relevant Lysine Acetylation Sites in alpha-Synuclein Enabled by Non-canonical Amino Acid Mutagenesis
Authors: Shimogawa, M. / Li, M.H. / Park, G.S.H. / Ramirez, J. / Lee, H. / Watson, P.R. / Sharma, S. / Lin, Z. / Peng, C. / Garcia, B. / Christianson, D. / Rhoades, E. / Eliezer, D. / Petersson, J.
History
DepositionJul 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Alpha-synuclein
A: Alpha-synuclein
B: 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)145,17110
Polymers145,17110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "E"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 36 - 96 / Label seq-ID: 36 - 96

Dom-IDAuth asym-IDLabel asym-ID
d_1EE
d_2BC
d_3CA
d_4DD
d_5AB
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.999078192653, 0.0428191463604, 0.00304723978408), (-0.0428231933686, 0.99908185218, 0.00127544274157), (-0.00298982859809, -0.00140475956759, 0.999994543773)-6.6681704706, 6.28599457345, 14.9992891406
2given(0.999514923567, 0.030982667998, -0.00316098889011), (-0.0309867380143, 0.999519018082, -0.00124681965499), (0.00312083871219, 0.00134416358677, 0.999994226778)-4.0817921241, 4.93217613574, 8.76643522714
3given(0.999825111737, 0.0183934603853, -0.00338031873573), (-0.018396937901, 0.999830261379, -0.0010005529141), (0.0033613413347, 0.00106256544301, 0.99999378615)-2.23606883037, 2.98779177985, 4.01011261459
4given(0.998403261108, 0.0564543536514, 0.0019581018519), (-0.0564539153036, 0.998405167207, -0.000278461261648), (-0.0019706993574, 0.000167474115619, 0.999998044146)-8.46581275297, 8.58963797328, 19.3488270525
5given(-0.998487662681, -0.0549658525556, 0.0010688906142), (0.0549683174764, -0.998485136123, 0.00243249157799), (0.000933567417, 0.00248756794883, 0.999996470223)304.757138605, 288.130315983, 16.0863636471
6given(-0.999280443439, -0.0378945201148, 0.00161267046118), (0.0378979426574, -0.999279307507, 0.00214744770375), (0.00153013172148, 0.00220701938633, 0.999996393875)302.228015687, 290.847961552, 11.2510109351
7given(-0.999659626056, -0.0260196243783, 0.0019003104515), (0.0260229715367, -0.999659798601, 0.00175841246272), (0.00185391073144, 0.00180726566973, 0.999996648397)300.515276585, 292.672253909, 6.5032946461
8given(-0.999947673691, -0.00994335030253, 0.00240409347704), (0.00994800509051, -0.999948650871, 0.00193204965306), (0.00238475898244, 0.00195586449018, 0.999995243748)298.105671467, 295.131062962, 1.63718169853
9given(-0.999989556079, 0.0040881528807, 0.00204321786801), (-0.00408361785841, -0.999989200406, 0.00221881422791), (0.00205226665387, 0.00221044733382, 0.999995451052)296.070162007, 297.180388861, -3.11531855228

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Components

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


Mass: 14517.138 Da / Num. of mol.: 10 / Mutation: K80(ALY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Variant: K80(ALY) / Production host: Escherichia coli (E. coli) / References: UniProt: P37840
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: alpha-synuclein, K80(ALY) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 0.1856 sec. / Electron dose: 14.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4038

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.58 ° / Axial rise/subunit: 2.38 Å / Axial symmetry: C1
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200042 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00184210
ELECTRON MICROSCOPYf_angle_d0.43995700
ELECTRON MICROSCOPYf_chiral_restr0.049750
ELECTRON MICROSCOPYf_plane_restr0.0014710
ELECTRON MICROSCOPYf_dihedral_angle_d9.3745659
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EEELECTRON MICROSCOPYNCS constraints1.69590735636E-13
ens_1d_3EEELECTRON MICROSCOPYNCS constraints1.31280371794E-13
ens_1d_4EEELECTRON MICROSCOPYNCS constraints5.39639272884E-14
ens_1d_5EEELECTRON MICROSCOPYNCS constraints2.19083742836E-13
ens_1d_6EEELECTRON MICROSCOPYNCS constraints9.16086216667E-11
ens_1d_7EEELECTRON MICROSCOPYNCS constraints2.33853646726E-13
ens_1d_8EEELECTRON MICROSCOPYNCS constraints5.37052896275E-11
ens_1d_9EEELECTRON MICROSCOPYNCS constraints1.94169031656E-11
ens_1d_10EEELECTRON MICROSCOPYNCS constraints6.77816816917E-12

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