8XIH | pdb_00008xih

protein-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb8XIH/pdb
• NAKB: 8XIH
• EM Map EMD-38373: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mucilaginibacter paludis DSM 18603
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-19 Released: 2024-12-25 
• Deposition Author(s): Li, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

protein-DNA complex

Zhuang, L.

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: 193.53 kDa 
• Atom Count: 11,418 
• Modeled Residue Count: 1,345 
• Deposited Residue Count: 1,621 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi domain-containing protein	A, B	795	Mucilaginibacter paludis DSM 18603	Mutation(s): 0
UniProt
Find proteins for H1YCU5 (Mucilaginibacter paludis DSM 18603) Explore H1YCU5  Go to UniProtKB:  H1YCU5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')	C [auth G]	8	Mucilaginibacter paludis DSM 18603

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')	D [auth H]	16	Mucilaginibacter paludis DSM 18603

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')	E	7	Mucilaginibacter paludis DSM 18603

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Li, Z.

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Funding Organization	Location	Grant Number
Not funded		NA

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release