9KCN | pdb_00009kcn

Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B

PDB DOI: https://doi.org/10.2210/pdb9KCN/pdb
EM Map EMD-62257: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

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: 2.60 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B

Zhang, S.Q., Liu, C.

To be published.

Macromolecule Content

Total Structure Weight: 140.41 kDa
Atom Count: 5,868
Modeled Residue Count: 804
Deposited Residue Count: 1,308
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	A C E G I A, C, E, G, I, K, M [auth S], O [auth U], Q [auth W], S [auth Y], U [auth a], W [auth c]	5	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	B [auth L] D [auth M] F [auth N] H [auth P] J [auth Q] B [auth L], D [auth M], F [auth N], H [auth P], J [auth Q], L [auth R], N [auth d], P [auth e], R [auth f], T [auth h], V [auth i], X [auth j]	104	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 AA [auth M] SDF format, chain BA [auth M] SDF format, chain CA [auth N] SDF format, chain DA [auth P] SDF format, chain EA [auth d] SDF format, chain FA [auth d] SDF format, chain GA [auth e] SDF format, chain HA [auth e] SDF format, chain IA [auth f] SDF format, chain JA [auth h] SDF format, chain Y [auth L] SDF format, chain Z [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth N] MOL2 format, chain DA [auth P] MOL2 format, chain EA [auth d] MOL2 format, chain FA [auth d] MOL2 format, chain GA [auth e] MOL2 format, chain HA [auth e] MOL2 format, chain IA [auth f] MOL2 format, chain JA [auth h] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain BA [auth M] mmCIF format, chain CA [auth N] mmCIF format, chain DA [auth P] mmCIF format, chain EA [auth d] mmCIF format, chain FA [auth d] mmCIF format, chain GA [auth e] mmCIF format, chain HA [auth e] mmCIF format, chain IA [auth f] mmCIF format, chain JA [auth h] mmCIF format, chain Y [auth L] mmCIF format, chain Z [auth L]	AA [auth M] BA [auth M] CA [auth N] DA [auth P] EA [auth d] AA [auth M], BA [auth M], CA [auth N], DA [auth P], EA [auth d], FA [auth d], GA [auth e], HA [auth e], IA [auth f], JA [auth h], Y [auth L], Z [auth L]	(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 AA [auth M] Focus chain BA [auth M] Focus chain CA [auth N] Focus chain DA [auth P] Focus chain EA [auth d] Focus chain FA [auth d] Focus chain GA [auth e] Focus chain HA [auth e] Focus chain IA [auth f] Focus chain JA [auth h] Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth M] Focus chain CA [auth N] Focus chain DA [auth P] Focus chain EA [auth d] Focus chain FA [auth d] Focus chain GA [auth e] Focus chain HA [auth e] Focus chain IA [auth f] Focus chain JA [auth h] Focus chain Y [auth L] Focus chain Z [auth L]