7F29 | pdb_00007f29

Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)

PDB DOI: https://doi.org/10.2210/pdb7F29/pdb
EM Map EMD-31428: EMDB EMDataResource

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

Deposited: 2021-06-10 Released: 2022-07-13
Deposition Author(s): Xia, W.C., Sun, Y.P., 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 7F29

This is version 1.1 of the entry. See complete history.

Literature

O-Glycosylation Induces Amyloid-beta To Form New Fibril Polymorphs Vulnerable for Degradation

Liu, D., Wei, Q., Xia, W., He, C., Zhang, Q., Huang, L., Wang, X., Sun, Y., Ma, Y., Zhang, X., Wang, Y., Shi, X., Liu, C., Dong, S.

(2021) J Am Chem Soc 143: 20216-20223

DOI: https://doi.org/10.1021/jacs.1c08607

Macromolecule Content

Total Structure Weight: 25.81 kDa
Atom Count: 1,794
Modeled Residue Count: 222
Deposited Residue Count: 222
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid-beta A4 protein	A [auth E] B [auth C] C [auth D] D [auth F] E [auth A] A [auth E], B [auth C], C [auth D], D [auth F], E [auth A], F [auth B]	37	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067 Go to UniProtKB: P05067
PHAROS: 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

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-alpha-D-galactopyranose	G, H, I, J, K G, H, I, J, K, L	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain O [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain P [auth F] SDF format, chain N [auth C] MOL2 format, chain M [auth E] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain P [auth F] MOL2 format, chain N [auth C] mmCIF format, chain M [auth E] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain P [auth F] mmCIF format, chain N [auth C]	M [auth E] N [auth C] O [auth D] P [auth F] Q [auth A] M [auth E], N [auth C], O [auth D], P [auth F], Q [auth A], R [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth F] Focus chain Q [auth A] Focus chain R [auth B] Interactions & Density Focus chain M [auth E] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth F] Focus chain Q [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-07-13
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection

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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.