9O4B | pdb_00009o4b

Cryo-EM structure of in-vitro alpha-synuclein fibril bound with Exemplar-6 PET-radioligand

PDB DOI: https://doi.org/10.2210/pdb9O4B/pdb
EM Map EMD-70093: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-04-08 Released: 2025-04-23
Deposition Author(s): Sanchez, J.C., Perez, R.M., Borcik, C.G., Guarino, D.S., Dhavala, D.D., Baumgardt, J.K., Shaffer, K.D., Kotzbauer, P.T., Mach, R.H., Rienstra, C.M., Petersson, E.J., Wright, E.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Complementary Structural and Chemical Biology Methods Reveal the Basis for Selective Radioligand Binding to Alpha-Synuclein in MSA Tissue

Sanchez, J.C., Perez, R.M., Borcik, C.G., Guarino, D.S., Dhavala, D.D., Baumgardt, J.K., Shaffer, K.D., Kotzbauer, P.T., Mach, R.H., Rienstra, C.M., Petersson, E.J., Wright, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 177.8 kDa
Atom Count: 5,940
Modeled Residue Count: 828
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	140	Homo sapiens	Mutation(s): 0 Gene Names: SNCA, NACP, PARK1
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens) Explore P37840 Go to UniProtKB: P37840
PHAROS: P37840 GTEx: ENSG00000145335
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37840
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1B9H (Subject of Investigation/LOI) Query on A1B9H Download:Ideal Coordinates CCD File SDF format, chain X [auth K] SDF format, chain W [auth J] SDF format, chain V [auth I] SDF format, chain U [auth H] SDF format, chain T [auth G] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain X [auth K] MOL2 format, chain W [auth J] MOL2 format, chain V [auth I] MOL2 format, chain U [auth H] MOL2 format, chain T [auth G] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain X [auth K] mmCIF format, chain W [auth J] mmCIF format, chain V [auth I] mmCIF format, chain U [auth H] mmCIF format, chain T [auth G] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A] N [auth A] O [auth B] P [auth C] Q [auth D] M [auth A], N [auth A], O [auth B], P [auth C], Q [auth D], R [auth E], S [auth F], T [auth G], U [auth H], V [auth I], W [auth J], X [auth K]	2-(3,4-dimethylphenoxy)-N-[3-(4-fluorophenyl)-1,2-oxazol-5-yl]acetamide C₁₉ H₁₇ F N₂ O₃ MVPTZZZADWKBAN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth K] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth K]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM139168
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM135066
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM149118
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	RF1NS110436
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM136463
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	RF1 NS103873
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM133398
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	F31 AG090063
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	U19-NS110456