9KCO | pdb_00009kco

Cryo-EM structure of FD4-bound alpha-synuclein MSA-like fibril

PDB DOI: https://doi.org/10.2210/pdb9KCO/pdb
EM Map EMD-62258: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-01 Released: 2025-11-05
Deposition Author(s): Zhang, S.Q., Liu, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 9KCO

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

Literature

Cryo-EM structure of FD4-bound alpha-synuclein MSA-like fibril

Zhang, S.Q., Liu, C.

To be published.

Macromolecule Content

Total Structure Weight: 180.01 kDa
Atom Count: 5,592
Modeled Residue Count: 744
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	A [auth F] B [auth G] C [auth H] D [auth I] E [auth J] A [auth F], B [auth G], C [auth H], D [auth I], E [auth J], F [auth K], G [auth L], H [auth M], I [auth N], J [auth O], K [auth P], L [auth Q]	140	Homo sapiens	Mutation(s): 2 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
A1EFL (Subject of Investigation/LOI) Query on A1EFL Download:Ideal Coordinates CCD File SDF format, chain M [auth G] SDF format, chain N [auth H] SDF format, chain O [auth I] SDF format, chain P [auth J] SDF format, chain Q [auth K] SDF format, chain R [auth K] SDF format, chain S [auth M] SDF format, chain T [auth N] SDF format, chain U [auth O] SDF format, chain V [auth P] SDF format, chain W [auth Q] SDF format, chain X [auth Q] MOL2 format, chain M [auth G] MOL2 format, chain N [auth H] MOL2 format, chain O [auth I] MOL2 format, chain P [auth J] MOL2 format, chain Q [auth K] MOL2 format, chain R [auth K] MOL2 format, chain S [auth M] MOL2 format, chain T [auth N] MOL2 format, chain U [auth O] MOL2 format, chain V [auth P] MOL2 format, chain W [auth Q] MOL2 format, chain X [auth Q] mmCIF format, chain M [auth G] mmCIF format, chain N [auth H] mmCIF format, chain O [auth I] mmCIF format, chain P [auth J] mmCIF format, chain Q [auth K] mmCIF format, chain R [auth K] mmCIF format, chain S [auth M] mmCIF format, chain T [auth N] mmCIF format, chain U [auth O] mmCIF format, chain V [auth P] mmCIF format, chain W [auth Q] mmCIF format, chain X [auth Q]	M [auth G] N [auth H] O [auth I] P [auth J] Q [auth K] M [auth G], N [auth H], O [auth I], P [auth J], Q [auth K], R [auth K], S [auth M], T [auth N], U [auth O], V [auth P], W [auth Q], X [auth Q]	(2~{R})-1-fluoranyl-3-[[2-[(~{E})-2-[5-[6-(methylamino)pyridin-3-yl]pyridin-2-yl]ethenyl]-1,3-benzothiazol-6-yl]oxy]propan-2-ol C₂₃ H₂₁ F N₄ O₂ S XQKIHSWMPMZBNJ-YXOJNZSOSA-N		Interactions Focus chain M [auth G] Focus chain N [auth H] Focus chain O [auth I] Focus chain P [auth J] Focus chain Q [auth K] Focus chain R [auth K] Focus chain S [auth M] Focus chain T [auth N] Focus chain U [auth O] Focus chain V [auth P] Focus chain W [auth Q] Focus chain X [auth Q] Interactions & Density Focus chain M [auth G] Focus chain N [auth H] Focus chain O [auth I] Focus chain P [auth J] Focus chain Q [auth K] Focus chain R [auth K] Focus chain S [auth M] Focus chain T [auth N] Focus chain U [auth O] Focus chain V [auth P] Focus chain W [auth Q] Focus chain X [auth Q]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.