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- PDB-9euu: Structure of recombinant alpha-synuclein fibrils 1B capable of se... -

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Basic information

Entry
Database: PDB / ID: 9euu
TitleStructure of recombinant alpha-synuclein fibrils 1B capable of seeding GCIs in vivo
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / aSyn / MSA
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / 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 / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / regulation of norepinephrine uptake / response to iron(II) ion / 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 / dopamine uptake involved in synaptic transmission / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / synaptic vesicle exocytosis / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / alpha-tubulin binding / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / excitatory postsynaptic potential / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / negative regulation of protein kinase activity / protein destabilization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / ferrous iron binding / tau protein binding / PKR-mediated signaling / positive regulation of protein serine/threonine kinase activity / receptor internalization / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / histone binding / cellular response to oxidative stress / growth cone / postsynapse / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / transcription cis-regulatory region binding
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.93 Å
AuthorsBurger, D. / Kashyrina, M. / Lewis, A. / De Nuccio, F. / Mohammed, I. / de La Seigliere, H. / van den Heuvel, L. / Feuillie, C. / Verchere, J. / Berbon, M. ...Burger, D. / Kashyrina, M. / Lewis, A. / De Nuccio, F. / Mohammed, I. / de La Seigliere, H. / van den Heuvel, L. / Feuillie, C. / Verchere, J. / Berbon, M. / Arotcarena, M. / Retailleau, A. / Bezard, E. / Laferriere, F. / Loquet, A. / Bousset, L. / Baron, T. / Lofrumento, D.D. / De Giorgi, F. / Stahlberg, H. / Ichas, F.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation514605 Switzerland
Citation
Journal: To Be Published
Title: Multiple System Atrophy: Insights from aSyn Fibril Structure
Authors: Burger, D. / Kashyrina, M. / Lewis, A. / De Nuccio, F. / Mohammed, I. / de La Seigliere, H. / van den Heuvel, L. / Feuillie, C. / Verchere, J. / Berbon, M. / Arotcarena, M. / Retailleau, A. ...Authors: Burger, D. / Kashyrina, M. / Lewis, A. / De Nuccio, F. / Mohammed, I. / de La Seigliere, H. / van den Heuvel, L. / Feuillie, C. / Verchere, J. / Berbon, M. / Arotcarena, M. / Retailleau, A. / Bezard, E. / Laferriere, F. / Loquet, A. / Bousset, L. / Baron, T. / Lofrumento, D.D. / De Giorgi, F. / Stahlberg, H. / Ichas, F.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: 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
D: Alpha-synuclein
A: Alpha-synuclein
B: Alpha-synuclein
E: Alpha-synuclein
F: Alpha-synuclein
G: Alpha-synuclein
H: Alpha-synuclein
O: Alpha-synuclein
N: Alpha-synuclein
P: Alpha-synuclein
Q: Alpha-synuclein
R: Alpha-synuclein
I: Alpha-synuclein
J: Alpha-synuclein
K: Alpha-synuclein
L: Alpha-synuclein
M: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)260,57018
Polymers260,57018
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "L"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "N"
d_13ens_1chain "M"
d_14ens_1chain "A"
d_15ens_1chain "O"
d_16ens_1chain "P"
d_17ens_1chain "Q"
d_18ens_1chain "R"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 37 - 97 / Label seq-ID: 37 - 97

Dom-IDAuth asym-IDLabel asym-ID
d_1LQ
d_2BD
d_3CA
d_4DB
d_5EE
d_6FF
d_7GG
d_8HH
d_9IN
d_10JO
d_11KP
d_12NJ
d_13MR
d_14AC
d_15OI
d_16PK
d_17QL
d_18RM

NCS oper:
IDCodeMatrixVector
1given(-0.997140639072, -0.0754774371369, 0.00370167461913), (0.0754810540312, -0.997146876273, 0.000847125883004), (0.00362717439286, 0.00112410994629, 0.999992789965)349.672600993, 324.50805853, 21.4859058044
2given(0.998751366409, 0.0499509251102, -0.000783055957931), (-0.0499514938687, 0.998751382217, -0.000724416533687), (0.000745892944314, 0.00076262681775, 0.999999431022)-8.17349836296, 8.82106066991, 14.579401662
3given(-0.998231483508, -0.0592256964473, 0.00512076302203), (0.0592382520931, -0.998241139757, 0.00233589072917), (0.00497341156027, 0.0026351047187, 0.999984160575)346.93097131, 327.217249978, 16.1017844482
4given(0.999476369292, 0.0323559451169, -0.000282918923513), (-0.032356397145, 0.99947482025, -0.00177404895309), (0.000225369309663, 0.00178227424363, 0.999998386352)-5.40233730454, 5.89232485405, 9.58876958983
5given(-0.999060493934, -0.0430434336032, 0.00503907577198), (0.0430582943155, -0.999068414353, 0.00287866846062), (0.00491047366657, 0.0030929379418, 0.99998316035)344.346710895, 330.036030084, 11.1153876261
6given(0.996263323611, 0.0863648593564, -0.000707880877999), (-0.0863647617646, 0.996263569503, 0.000167349569734), (0.000719689052352, -0.000105588275162, 0.999999735449)-13.8881730174, 15.1960784725, 24.5782549333
7given(-0.995613413654, -0.0935228810876, 0.00272052669942), (0.0935217225165, -0.995617087341, -0.000550284119631), (0.00276006702479, -0.000293441907743, 0.999996147954)352.600875142, 321.459288045, 26.7717315003
8given(0.990585297381, 0.136876285661, -0.00237719064798), (-0.136867888637, 0.990583491822, 0.00339511252088), (0.00281951620406, -0.00303778748126, 0.999991411051)-21.2314613757, 24.224947044, 39.5437970414
9given(0.994796033641, 0.101886445248, 6.10478106233E-5), (-0.101886458842, 0.994795991127, 0.000292475141186), (-3.09308648164E-5, -0.000297173055635, 0.999999955366)-16.3819454274, 18.0636445665, 29.6814129878
10given(0.999868123431, 0.016224393428, -0.000710495482226), (-0.0162260322483, 0.999865552296, -0.00236499647191), (0.000672029324524, 0.0023762131069, 0.999996950989)-2.61538937019, 3.13275027632, 4.47825670693
11given(-0.999909624413, -0.00534686300906, 0.0123350744657), (0.0054111829066, -0.999971907076, 0.00518692188734), (0.0123069941766, 0.00525320046033, 0.999910466882)337.036672293, 336.182417451, -0.292070703993
12given(0.992895487135, 0.118981948553, -0.00135924470552), (-0.118981053932, 0.992896262662, 0.000721385129353), (0.0014354207965, -0.000554535671807, 0.999998816028)-18.7194711973, 21.2103049386, 34.4101570002
13given(0.997652333839, 0.0684787528623, -0.000693679758568), (-0.0684786910204, 0.997652572898, 0.000112540654743), (0.000699758039586, -6.47741650022E-5, 0.999999753071)-11.0904624807, 11.9663739356, 19.6499352461
14given(-0.999666010355, -0.0252892442863, 0.00532182905077), (0.0253019669625, -0.999677122192, 0.0023370568435), (0.00526100834884, 0.00247092903353, 0.999983108008)341.373480644, 333.233455323, 6.23001899226
15given(-0.994160674965, -0.107800377444, 0.00486117030605), (0.107798696411, -0.994172556587, -0.000607273624477), (0.00489830643711, -7.96997343722E-5, 0.999988000049)354.431179264, 318.795867814, 31.3537653442
16given(-0.992282886145, -0.123920847755, 0.00427754091251), (0.123926728132, -0.992290719968, 0.00113715413907), (0.00410364704683, 0.00165848024085, 0.999990204714)356.931428711, 315.461309371, 36.1277010367
17given(-0.989808407755, -0.142320369799, 0.00492222279799), (0.142327252869, -0.989819072268, 0.00107576254833), (0.00471900707971, 0.00176536526393, 0.999987307148)359.509460133, 311.947403737, 40.9388576227

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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.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P37840

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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: recombinant alpha-synuclein fibril / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 14 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.4 / Details: NaCl 100 mM, TRIS 20mM
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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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: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1RELION4.0.0particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Cootmodel fitting
13PHENIXdev_5240model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.52 ° / Axial rise/subunit: 2.36 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 108543
Details: particles selected by manual picking of fibril start and end points
3D reconstructionResolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51272 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 9.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217614
ELECTRON MICROSCOPYf_angle_d0.571910296
ELECTRON MICROSCOPYf_chiral_restr0.05721368
ELECTRON MICROSCOPYf_plane_restr0.00131260
ELECTRON MICROSCOPYf_dihedral_angle_d4.99121098
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2QLELECTRON MICROSCOPYNCS constraints1.33921634903E-10
ens_1d_3QLELECTRON MICROSCOPYNCS constraints1.53362420984E-13
ens_1d_4QLELECTRON MICROSCOPYNCS constraints9.5084969002E-11
ens_1d_5QLELECTRON MICROSCOPYNCS constraints2.00114445052E-10
ens_1d_6QLELECTRON MICROSCOPYNCS constraints6.97286004333E-11
ens_1d_7QLELECTRON MICROSCOPYNCS constraints1.64337733356E-10
ens_1d_8QLELECTRON MICROSCOPYNCS constraints1.62262384839E-13
ens_1d_9QLELECTRON MICROSCOPYNCS constraints1.86313999752E-10
ens_1d_10QLELECTRON MICROSCOPYNCS constraints3.92404621487E-11
ens_1d_11QLELECTRON MICROSCOPYNCS constraints3.12455862528E-10
ens_1d_12QLELECTRON MICROSCOPYNCS constraints2.8529857221E-13
ens_1d_13QLELECTRON MICROSCOPYNCS constraints2.92732231684E-10
ens_1d_14QLELECTRON MICROSCOPYNCS constraints1.63120394915E-10
ens_1d_15QLELECTRON MICROSCOPYNCS constraints9.85662127552E-11
ens_1d_16QLELECTRON MICROSCOPYNCS constraints1.0143360627E-12
ens_1d_17QLELECTRON MICROSCOPYNCS constraints1.18685838775E-10
ens_1d_18QLELECTRON MICROSCOPYNCS constraints1.36373208864E-10

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