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

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Basic information

Entry
Database: PDB / ID: 9hca
TitleThe L2A-II alpha-synuclein fibril in the presence of MODAG-005 (long 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: 2.7 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(0.999944578718, 0.0105252357375, 0.000242704925527), (-0.0105251835528, 0.999944585544, -0.000215296959119), (-0.000244957527414, 0.000212730513195, 0.999999947371)-1.40517782878, 1.41696506745, 4.69539073711
2given(0.999780799407, 0.020936841515, 4.2473846605E-5), (-0.020936861665, 0.999780649627, 0.000548138691838), (-3.09882370316E-5, -0.000548907808563, 0.99999984887)-2.72761366656, 2.6989271997, 9.48036897511
3given(0.999507305275, 0.0313862094823, 0.000229251965013), (-0.0313861587151, 0.999507308553, -0.000221787188271), (-0.000236100073682, 0.000214482576334, 0.999999949127)-4.08195090623, 4.21538515648, 14.0939235977
4given(0.99912580626, 0.041803975986, 0.000225513253411), (-0.0418039282097, 0.999125811098, -0.000212567133331), (-0.000234202263565, 0.000202953968617, 0.999999951979)-5.39764300146, 5.63265266034, 18.7953202975
5given(-0.499886583029, 0.866090652952, 0.000620464930499), (-0.866090830451, -0.49988665922, -3.66526372335E-5), (0.000278417634756, -0.000555701148507, 0.99999980684)83.0833464416, 310.556134978, 0.0616147319438
6given(-0.508964341071, 0.86078754842, 0.000309844514031), (-0.860787603466, -0.508964322383, -0.000142338884821), (3.51762634182E-5, -0.000339155733401, 0.999999941868)85.0144763498, 311.064053009, 4.75599993527
7given(-0.517921645721, 0.85542799926, 0.000327071686482), (-0.855428061673, -0.517921614066, -0.000181621165452), (1.40336655923E-5, -0.000373851831703, 0.999999930019)86.8940028384, 311.540405187, 9.46352361387
8given(-0.526818356569, 0.849977831953, 0.000323063615973), (-0.849977891432, -0.526818342853, -0.000133077598518), (5.70828301336E-5, -0.000344704652851, 0.99999993896)88.7812022032, 311.98434697, 14.1544162568
9given(-0.535657232586, 0.844435450712, 0.00031425972133), (-0.844435507551, -0.535657217627, -0.000137077729283), (5.25821938299E-5, -0.000338798744401, 0.999999941225)90.6731755879, 312.416203132, 18.8536105779
10given(-0.500266138411, -0.865871638912, -0.000309334954492), (0.865871692379, -0.500266082494, -0.000242987101122), (5.56458536203E-5, -0.00038940259932, 0.999999922635)310.614141655, 83.31724382, 0.0530977580975
11given(-0.491132555343, -0.871084813804, -0.000245441770052), (0.871084826148, -0.491132586974, 8.75613535794E-5), (-0.000196817816856, -0.000170796370262, 0.999999966046)310.088846183, 81.3906633021, 4.74814313212
12given(-0.482012478482, -0.876164320737, -0.00023163546356), (0.876164333479, -0.482012505209, 7.45811531141E-5), (-0.000176996535444, -0.000167001685079, 0.999999970391)309.554140685, 79.5279602267, 9.44527879271
13given(-0.4728439786, -0.881146138197, -0.000234610363825), (0.881146150992, -0.472844006414, 7.86760362826E-5), (-0.000180259189916, -0.000169524529051, 0.999999969384)309.002455966, 77.6693754704, 14.145957649
14given(-0.463638468083, -0.886024406716, -0.000348738070518), (0.886024430103, -0.463638534278, 0.000137088704394), (-0.00028315234584, -0.000245430853289, 0.999999929794)308.448425973, 75.8107021259, 18.8680602202

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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 (long 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108610 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01457575
ELECTRON MICROSCOPYf_angle_d2.123410215
ELECTRON MICROSCOPYf_chiral_restr0.09891365
ELECTRON MICROSCOPYf_plane_restr0.00511245
ELECTRON MICROSCOPYf_dihedral_angle_d19.38772580
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.000509099552331
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000510639818799
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000518677032944
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000514587421117
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000496930324717
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.00051131873866
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.000509252069773
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.000498483327705
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.000502969499791
ens_1d_11AAELECTRON MICROSCOPYNCS constraints0.000516674255988
ens_1d_12AAELECTRON MICROSCOPYNCS constraints0.00050346111175
ens_1d_13AAELECTRON MICROSCOPYNCS constraints0.00050574256816
ens_1d_14AAELECTRON MICROSCOPYNCS constraints0.000502916501535
ens_1d_15AAELECTRON MICROSCOPYNCS constraints0.000509799757827

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