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- PDB-9tpt: Structure of recombinantly assembled E83Q alpha-synuclein fibrils -

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Basic information

Entry
Database: PDB / ID: 9tpt
TitleStructure of recombinantly assembled E83Q alpha-synuclein fibrils
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / E83Q / Alpha-synuclein / Fibrils / Recombinant
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 / positive regulation of protein localization to cell periphery / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / dopamine biosynthetic process / response to iron(II) ion / SNARE complex assembly / negative regulation of dopamine metabolic process / positive regulation of neurotransmitter secretion / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / regulation of locomotion / synaptic vesicle transport / negative regulation of microtubule polymerization / 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 / positive regulation of receptor recycling / dynein complex binding / 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 / cysteine-type endopeptidase inhibitor activity / response to type II interferon / negative regulation of serotonin uptake / regulation of presynapse assembly / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / cellular response to fibroblast growth factor stimulus / phospholipid metabolic process / axon terminus / inclusion body / cellular response to epinephrine stimulus / Hsp70 protein binding / enzyme inhibitor activity / 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 / ferrous iron binding / microglial cell activation / 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 / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / long-term synaptic potentiation / 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 / oxidoreductase activity / mitochondrial outer membrane
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsShafiei, N. / Mohammed, I. / Kumar, S.T. / Mahul Mellier, A.L. / Ekundayo, B. / Stahli, D. / Lewis, A.J. / Stahlberg, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Structure of recombinantly assembled E83Q alpha-synuclein fibrils
Authors: Shafiei, N. / Mohammed, I. / Kumar, S.T. / Mahul Mellier, A.L. / Ekundayo, B. / Stahli, D. / Lewis, A.J. / Stahlberg, H.
History
DepositionDec 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 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
B: Alpha-synuclein
F: Alpha-synuclein
E: Alpha-synuclein
A: Alpha-synuclein
D: Alpha-synuclein
C: Alpha-synuclein
I: Alpha-synuclein
N: Alpha-synuclein
M: Alpha-synuclein
L: Alpha-synuclein
H: Alpha-synuclein
J: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)77,04412
Polymers77,04412
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_1(chain "E" and resid 36 through 99)
d_2ens_1(chain "B" and resid 36 through 99)
d_3ens_1(chain "C" and resid 36 through 99)
d_4ens_1(chain "D" and resid 36 through 99)
d_5ens_1(chain "A" and resid 36 through 99)
d_6ens_1(chain "F" and resid 36 through 99)
d_7ens_1chain "H"
d_8ens_1chain "I"
d_9ens_1chain "J"
d_10ens_1chain "L"
d_11ens_1chain "M"
d_12ens_1chain "N"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 36 - 99 / Label seq-ID: 1 - 64

Dom-IDAuth asym-IDLabel asym-ID
d_1EC
d_2BA
d_3CF
d_4DE
d_5AD
d_6FB
d_7HK
d_8IG
d_9JL
d_10LJ
d_11MI
d_12NH

NCS oper:
IDCodeMatrixVector
1given(0.999504539055, 0.0314305207818, -0.00167295297238), (-0.0314276324825, 0.999504540308, 0.00172563589864), (0.00172636172659, -0.00167220396228, 0.9999971117)-5.13778820348, 4.87955876791, 9.78517474183
2given(0.997876930546, 0.0634710286219, 0.0145965752859), (-0.0636299842231, 0.997916240711, 0.010695869939), (-0.0138872816695, -0.0116019417194, 0.999836255772)-12.6031959277, 9.3949308031, 19.3293770807
3given(0.997108267944, 0.0758684381847, -0.00436830454606), (-0.0758696986661, 0.997117733076, -0.000123327414878), (0.004346357268, 0.00045439273463, 0.999990451307)-11.6521915268, 13.0603263442, 18.758775597
4given(0.999696602107, 0.0239972018873, 0.00555320072271), (-0.0240264168628, 0.999697510256, 0.00525540497805), (-0.00542540592218, -0.00538723401474, 0.999970770913)-4.67263721989, 3.28174290903, 6.87020858678
5given(0.999759525707, -0.0187217411111, 0.0114187200525), (0.0186175012356, 0.999784646399, 0.00916784990099), (-0.0115878991024, -0.00895305723408, 0.999892775932)1.30982533873, -4.54253022307, -1.27606099527
6given(-0.999328148971, -0.0354245619865, -0.00939952567766), (0.0355181604204, -0.999319148102, -0.00998501464202), (-0.00903941122264, -0.0103121600605, 0.999905969779)344.085185204, 332.30508674, 10.8386634415
7given(-0.998945635722, -0.0453350867372, -0.00723510763182), (0.0454013286404, -0.998925814758, -0.00927016551245), (-0.0068070720284, -0.00958887488042, 0.999930856234)345.588817605, 330.757553095, 15.1526449986
8given(-0.997958067538, -0.0638007541962, -0.003026416833), (0.0638219674823, -0.997932928914, -0.00752501538747), (-0.00254005935721, -0.00770280169098, 0.999967106931)347.866877194, 327.220658329, 18.9592628232
9given(-0.999984720636, -0.00473386923303, 0.00285464140923), (0.00473037990539, -0.999988057873, -0.00122785032091), (0.0028604198016, -0.00121432802178, 0.999995171691)337.345184044, 336.41266804, 2.12223280275
10given(-0.999879774134, 0.00769821771919, -0.0134601159266), (-0.00755238000824, -0.999912591078, -0.0108522697917), (-0.013542482528, -0.0107493091578, 0.999850515587)337.7311272, 339.86717084, 1.9187256275
11given(-0.999492912283, 0.0276206915443, -0.0158434748407), (-0.0274114618716, -0.99953609044, -0.013274624889), (-0.0162027792207, -0.0128336006833, 0.999786361499)334.74557231, 343.422043774, -2.16570557046

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Components

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


Mass: 6420.322 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli (E. coli) / 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: alpha-synuclein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryFitting-ID
1RELIONparticle selection
13RELION4.0.03D reconstruction
14PHENIX1.20.1model refinement1
15Coot0.9.8.91model fitting2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.43 ° / Axial rise/subunit: 2.45 Å / Axial symmetry: C1
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6125 / Symmetry type: HELICAL
Atomic model building
ID
1
2
Atomic model building
IDPDB-ID 3D fitting-IDSource nameType
17UAK

7uak

1PDBexperimental model
27UAK

7uak

2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.88 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325376
ELECTRON MICROSCOPYf_angle_d0.64167266
ELECTRON MICROSCOPYf_chiral_restr0.0586948
ELECTRON MICROSCOPYf_plane_restr0.003906
ELECTRON MICROSCOPYf_dihedral_angle_d5.0529774
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CEELECTRON MICROSCOPYNCS constraints2.93062511227E-13
ens_1d_3CEELECTRON MICROSCOPYNCS constraints3.12697255098E-13
ens_1d_4CEELECTRON MICROSCOPYNCS constraints3.92907489716E-13
ens_1d_5CEELECTRON MICROSCOPYNCS constraints3.64745410206E-13
ens_1d_6CEELECTRON MICROSCOPYNCS constraints2.76974371808E-13
ens_1d_7CEELECTRON MICROSCOPYNCS constraints2.73250942038E-13
ens_1d_8CEELECTRON MICROSCOPYNCS constraints3.03014824255E-13
ens_1d_9CEELECTRON MICROSCOPYNCS constraints3.63422094659E-13
ens_1d_10CEELECTRON MICROSCOPYNCS constraints3.69970734752E-11
ens_1d_11CEELECTRON MICROSCOPYNCS constraints2.8664778443E-13
ens_1d_12CEELECTRON MICROSCOPYNCS constraints2.46309012498E-13

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