9XJC | pdb_00009xjc

The cryo-EM structure of ThT bound type1 amyloid beta 42 fibril

PDB DOI: https://doi.org/10.2210/pdb9XJC/pdb
EM Map EMD-66934: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2025-11-04 Released: 2026-11-11
Deposition Author(s): Zhao, Q.Y., Cao, T.Y., Liu, C., Li, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 9XJC

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

Literature

The cryo-EM structure of ThT bound type1 amyloid beta fibril

Zhao, Q.Y., Cao, T.Y., Liu, C., Li, D.

To be published.

Macromolecule Content

Total Structure Weight: 522.56 kDa
Atom Count: 1,520
Modeled Residue Count: 204
Deposited Residue Count: 4,620
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid-beta precursor protein	A [auth C] B [auth D] C [auth E] D [auth F] E [auth A] A [auth C], B [auth D], C [auth E], D [auth F], E [auth A], F [auth B]	770	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067 Go to UniProtKB: P05067
GTEx: ENSG00000142192
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05067
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TFX (Subject of Investigation/LOI) Query on TFX Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium C₁₇ H₁₉ N₂ S FXEKRIDRIFBJOR-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.15.2_3472
RECONSTRUCTION	RELION

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release