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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 / 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 / actin binding / response to lipopolysaccharide / growth cone / cellular response to oxidative stress / histone binding / cell cortex / amyloid fibril formation / microtubule binding / oxidoreductase activity / 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: 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: Nature / Year: 2025
Title: Synthetic α-synuclein fibrils replicate in mice causing MSA-like pathology.
Authors: Domenic Burger / Marianna Kashyrina / Lukas van den Heuvel / Hortense de La Seiglière / Amanda J Lewis / Francesco De Nuccio / Inayathulla Mohammed / Jérémy Verchère / Cécile Feuillie / ...Authors: Domenic Burger / Marianna Kashyrina / Lukas van den Heuvel / Hortense de La Seiglière / Amanda J Lewis / Francesco De Nuccio / Inayathulla Mohammed / Jérémy Verchère / Cécile Feuillie / Mélanie Berbon / Marie-Laure Arotcarena / Aude Retailleau / Erwan Bezard / Marie-Hélène Canron / Wassilios G Meissner / Antoine Loquet / Luc Bousset / Christel Poujol / K Peter R Nilsson / Florent Laferrière / Thierry Baron / Dario Domenico Lofrumento / Francesca De Giorgi / Henning Stahlberg / François Ichas /
Abstract: Multiple-system atrophy (MSA) is a rapidly progressive neurodegenerative disease of unknown cause, typically affecting individuals aged 50-60 years and leading to death within a decade. It is ...Multiple-system atrophy (MSA) is a rapidly progressive neurodegenerative disease of unknown cause, typically affecting individuals aged 50-60 years and leading to death within a decade. It is characterized by glial cytoplasmic inclusions (GCIs) composed of fibrillar α-synuclein (aSyn), the formation of which shows parallels with prion propagation. While fibrils extracted from brains of individuals with MSA have been structurally characterized, their ability to replicate in a protein-only manner has been questioned, and their ability to induce GCIs in vivo remains unexplored. By contrast, the synthetic fibril strain 1B, assembled from recombinant human aSyn, self-replicates in vitro and induces GCIs in mice-suggesting direct relevance to MSA-but lacks scrutiny at the atomic scale. Here we report high-resolution structural analyses of 1B fibrils and of fibrils extracted from diseased mice injected with 1B that developed GCIs (1B). We show in vivo that conformational templating enables fibril strain replication, resulting in MSA-like inclusion pathology. Notably, the structures of 1B and 1B are highly similar and mimic the fold of aSyn observed in one protofilament of fibrils isolated from patients with MSA. Moreover, reinjection of crude mouse brain homogenates containing 1B into new mice reproduces the same MSA-like pathology induced by the parent synthetic seed 1B. Our findings identify 1B as a synthetic pathogen capable of self-replication in vivo and reveal structural features of 1B and 1B that may underlie MSA pathology, offering insights for therapeutic strategies.
#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
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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 (eV)
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
Has protein modificationN

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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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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

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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

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