ISDA: 9QCC

Deposition Date 2025-03-04

Release Date 2025-12-17

Last Version Date 2025-12-17

Entry Detail

PDB ID:

9QCC

Keywords:

RNA BINDING PROTEIN

Title:

Activated XauSPARDA filament assembly with bound dsDNA substrate

Biological Source:

Source Organism:

Xanthobacter autotrophicus Py2 (Taxon ID: 78245)
Escherichia coli (Taxon ID: 562)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DUF4365 domain-containing protein
Gene (Uniprot):Xaut_0433
Chain IDs:A, E, I, M, Q, U, Z (auth: W), CA (auth: Y)
Chain Length:458
Number of Molecules:8
Biological Source:Xanthobacter autotrophicus Py2

UniProt ID:A7ICE8 Pfam ID:PF14280

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein argonaute
Gene (Uniprot):Xaut_0434
Chain IDs:B, F, J, N, R, V, Y (auth: X), DA (auth: Z)
Chain Length:482
Number of Molecules:8
Biological Source:Xanthobacter autotrophicus Py2

UniProt ID:A7ICE9

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*TP*TP*CP*GP*GP*CP*CP*GP*TP*GP*TP*AP*CP*AP*AP*T)-3')
Chain IDs:C, G, K, O, S (auth: 1), W (auth: 3), AA (auth: 5), EA (auth: 7)
Chain Length:17
Number of Molecules:8
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*AP*UP*UP*GP*UP*AP*CP*AP*CP*GP*GP*CP*CP*GP*AP*AP*U)-3')
Chain IDs:D, H, L, P, T (auth: 2), X (auth: 4), BA (auth: 6), FA (auth: 8)
Chain Length:17
Number of Molecules:8
Biological Source:Escherichia coli

Polymer Type:polydeoxyribonucleotide
Molecule:dsDNA substrate, first strand
Chain IDs:GA (auth: S)
Chain Length:42
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polydeoxyribonucleotide
Molecule:dsDNA substrate, second strand
Chain IDs:HA (auth: T)
Chain Length:42
Number of Molecules:1
Biological Source:Escherichia coli

Ligand Molecules

Primary Citation

Activation of the SPARDA defense system by filament assembly using a beta-relay signaling mechanism widespread in prokaryotic Argonautes.

Jurgelaitis, E, Zagorskaite, E, Kopustas, A, Asmontas, S, Manakova, E, Dalgediene, I, Tylenyte, U, Silanskas, A, Toliusis, P, Grybauskas, A, Tutkus, M, Venclovas, C, Zaremba, M.Show

Cell Res. ? ? ? (2025)

PMID: 41298897 DOI: 10.1038/s41422-025-01198-1

Primary Citation of related structures

Feedback Form