8JSI | pdb_00008jsi

Cryo-EM structure of a DNA-protein complex

• PDB DOI: https://doi.org/10.2210/pdb8JSI/pdb
• EM Map EMD-36621: EMDB EMDataResource
• NAKB: 8JSI

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Thermococcus thioreducens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-20 Released: 2024-06-26 
• Deposition Author(s): Li, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a DNA-protein complex

Li, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 194.78 kDa 
• Atom Count: 13,377 
• Modeled Residue Count: 1,530 
• Deposited Residue Count: 1,564 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argonaute family protein	A, D [auth B]	750	Thermococcus thioreducens	Mutation(s): 0  Gene Names: A3L14_06700
UniProt
Find proteins for A0A0Q2M2Z1 (Thermococcus thioreducens) Explore A0A0Q2M2Z1  Go to UniProtKB:  A0A0Q2M2Z1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*C)-3')	B [auth T], E [auth U]	16	Thermococcus thioreducens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')	C [auth G], F [auth H]	16	Thermococcus thioreducens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	H [auth A], I [auth T], J [auth G], K [auth B], L [auth U], M [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Li, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection, Structure summary