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- PDB-9hc7: The L2A-II alpha-synuclein fibril in the presence of MODAG-005 (s... -

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Basic information

Entry
Database: PDB / ID: 9hc7
TitleThe L2A-II alpha-synuclein fibril in the presence of MODAG-005 (short incubation)
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / fibril / MODAG-005 / PET tracer
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / 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 ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / 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 / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / 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 / dopamine biosynthetic process / response to iron(II) ion / positive regulation of neurotransmitter secretion / SNARE complex assembly / negative regulation of dopamine metabolic process / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / regulation of locomotion / synaptic vesicle transport / transporter regulator activity / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / mitochondrial ATP synthesis coupled electron transport / dynein complex binding / positive regulation of receptor recycling / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / synaptic vesicle endocytosis / enzyme inhibitor activity / cysteine-type endopeptidase inhibitor activity / regulation of presynapse assembly / response to type II interferon / negative regulation of serotonin uptake / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / axon terminus / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / adult locomotory behavior / excitatory postsynaptic potential / protein tetramerization / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / regulation of long-term neuronal synaptic plasticity / synapse organization / PKR-mediated signaling / protein destabilization / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / actin cytoskeleton / growth cone / actin binding / cellular response to oxidative stress / neuron apoptotic process / cell cortex / histone binding / response to lipopolysaccharide / microtubule binding / chemical synaptic transmission / amyloid fibril formation / molecular adaptor activity / negative regulation of neuron apoptotic process / mitochondrial outer membrane / oxidoreductase activity
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsFrieg, B. / Kim, M. / Griesinger, C. / Schroeder, G.F.
Funding support Germany, 3items
OrganizationGrant numberCountry
Helmholtz Association Germany
Max Planck Society Germany
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Structural insights into binding of novel PET tracer MODAG-005 to lipidic alpha-synuclein fibrils
Authors: Kim, M. / Matthes, D. / Frieg, B. / Leonov, A. / Ryazanov, S. / Bleher, D. / Grotegerd, A.-K. / Dienemann, C. / Giese, A. / Schroeder, G.F. / Becker, S. / Herfert, K. / de Groot, B.L. / ...Authors: Kim, M. / Matthes, D. / Frieg, B. / Leonov, A. / Ryazanov, S. / Bleher, D. / Grotegerd, A.-K. / Dienemann, C. / Giese, A. / Schroeder, G.F. / Becker, S. / Herfert, K. / de Groot, B.L. / Andreas, L.B. / Griesinger, C.
History
DepositionNov 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data 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
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
K: Alpha-synuclein
L: Alpha-synuclein
M: Alpha-synuclein
N: Alpha-synuclein
O: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)217,14215
Polymers217,14215
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 "A"
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 "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"

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: 15 - 96 / Label seq-ID: 15 - 96

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ
d_11KK
d_12LL
d_13MM
d_14NN
d_15OO

NCS oper:
IDCodeMatrixVector
1given(0.999944904653, 0.0104956818436, 0.00016828657656), (-0.0104956575426, 0.999944908608, -0.00014464087805), (-0.000169795410056, 0.000142866630734, 0.999999975379)-1.39196819463, 1.40258503542, 4.69752186366
2given(0.999781202824, 0.0209175645118, -4.44378374518E-5), (-0.0209175334744, 0.999781017673, 0.000611140949189), (5.72116865812E-5, -0.000610077703323, 0.999999812266)-2.71567788602, 2.68725162946, 9.47970300913
3given(0.99950824107, 0.0313568101092, 0.000162769413191), (-0.0313567860707, 0.999508244091, -0.000148194207902), (-0.000167336268007, 0.000143017406408, 0.999999975772)-4.07192163197, 4.19831664087, 14.0972943917
4given(0.999126963493, 0.0417766093247, 0.000160417360984), (-0.0417765853081, 0.999126966078, -0.000150255603985), (-0.000166554480852, 0.000143422735792, 0.999999975845)-5.38917871567, 5.61627773476, 18.7971551988
5given(-0.4998850016, 0.866091688785, 0.000414479535957), (-0.866091740772, -0.499884759144, -0.000569334613941), (-0.00028590397427, -0.000643579137212, 0.999999752032)83.1189241038, 310.587798423, 0.147045591472
6given(-0.508942865016, 0.860800275901, 0.000212504429463), (-0.860800183133, -0.508942649344, -0.00065145758432), (-0.000452622300992, -0.000514478541199, 0.999999765222)85.0297370508, 311.09010749, 4.84603799631
7given(-0.517902314805, 0.855439740681, 0.000205871372893), (-0.855439649465, -0.517902104261, -0.000645387902624), (-0.000445469242831, -0.000510358423779, 0.999999770546)86.9116252949, 311.559359302, 9.54448241743
8given(-0.52679332308, 0.849993381655, 0.000214246596578), (-0.849993296097, -0.526793106869, -0.00064741468463), (-0.000437434566874, -0.00052316190393, 0.999999767476)88.7945298875, 312.008804459, 14.2454234308
9given(-0.535633457318, 0.844450565494, 0.00020454473614), (-0.84445047751, -0.535633244911, -0.000646512825543), (-0.000436387160381, -0.000519021800052, 0.999999770091)90.6854547917, 312.439014188, 18.9444071
10given(-0.500263416534, -0.865872823629, -0.000876001147624), (0.865873255885, -0.500263314529, -0.000347677333211), (-0.000137186883422, -0.000932436216416, 0.999999555871)310.658714242, 83.3046569066, 0.14962891532
11given(-0.491154743455, -0.871071931728, -0.000841271357831), (0.871072282753, -0.491154827148, -0.000118279132426), (-0.000310164855975, -0.000790901519023, 0.999999639136)310.137293019, 81.3962456289, 4.84739333745
12given(-0.482038440629, -0.876149676828, -0.000827979375237), (0.876150019934, -0.482038512122, -0.000124098647438), (-0.00029038895626, -0.000785254464614, 0.999999649525)309.6014509, 79.532466115, 9.5441630447
13given(-0.472869901578, -0.881131864838, -0.000832435876813), (0.881132210089, -0.472869976532, -0.000116782519052), (-0.000290733134741, -0.000788709002184, 0.999999646706)309.048746768, 77.6725799642, 14.2446171971
14given(-0.463665583526, -0.886009780633, -0.000946190559285), (0.886010201391, -0.463665741251, -5.84924551999E-5), (-0.000386891259636, -0.000865455426359, 0.999999550651)308.493344337, 75.8134786945, 18.9659694505

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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.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli BL21(DE3) (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: The L2A-II alpha-synuclein fibril in the presence of MODAG-005 (short incubation)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 2300 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.6 ° / Axial rise/subunit: 4.7 Å / Axial symmetry: C3
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130611 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01457575
ELECTRON MICROSCOPYf_angle_d2.134710215
ELECTRON MICROSCOPYf_chiral_restr0.09891365
ELECTRON MICROSCOPYf_plane_restr0.00531245
ELECTRON MICROSCOPYf_dihedral_angle_d19.20762580
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.000494807593306
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000500816661206
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000499436658924
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000507573409705
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000500360174198
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.000499819428295
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.000507103722459
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.00050005352126
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.000509322918907
ens_1d_11AAELECTRON MICROSCOPYNCS constraints0.000492007032963
ens_1d_12AAELECTRON MICROSCOPYNCS constraints0.000488103426167
ens_1d_13AAELECTRON MICROSCOPYNCS constraints0.000501242340691
ens_1d_14AAELECTRON MICROSCOPYNCS constraints0.000492984438564
ens_1d_15AAELECTRON MICROSCOPYNCS constraints0.000497886701978

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