8K88

Structure of procaryotic Ago

• PDB DOI: https://doi.org/10.2210/pdb8K88/pdb
• NAKB: 8K88
• EM Map EMD-36947: EMDB EMDataResource

• Classification: DNA/RNA/CELL INVASION
• Organism(s): synthetic construct, Geobacter sulfurreducens
• Expression System: Expression vector pET-mod
• Mutation(s): No 


• Deposited: 2023-07-29 Released: 2024-07-03 
• Deposition Author(s): Gao, X., Sun, D., Cui, S., Wang, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Basis of prokaryotic Argonaute System

Gao, X., Cui, S., Sun, D., Wang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 139.2 kDa 
• Atom Count: 6,686 
• Modelled Residue Count: 770 
• Deposited Residue Count: 1,122 
• Unique protein chains: 2
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi domain protein	C [auth A]	473	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: GSU1361
UniProt
Find proteins for Q74DF5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74DF5  Go to UniProtKB:  Q74DF5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sir2 superfamily protein	D [auth B]	587	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: GSU1360
UniProt
Find proteins for Q74DF6 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74DF6  Go to UniProtKB:  Q74DF6

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (41-mer)	A [auth C]	41	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (21-mer)	B [auth D]	21	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Gao, X., Sun, D., Cui, S., Wang, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release