8K21 | pdb_00008k21

Cas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex

• PDB DOI: https://doi.org/10.2210/pdb8K21/pdb
• NAKB: 8K21
• EM Map EMD-36824: EMDB EMDataResource

• Classification: ANTIBIOTIC/RNA BINDING PROTEIN/DNA
• Organism(s): Vibrio phage ICP1_2004_A
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2024-07-17 
• Deposition Author(s): Zhang, L.X., Feng, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of csy complex with short DNA

Zhang, L.X., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 163.5 kDa 
• Atom Count: 11,389 
• Modeled Residue Count: 1,372 
• Deposited Residue Count: 1,372 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HD Cas3-type domain-containing protein	C [auth A], F [auth a]	75	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00455
UniProt
Find proteins for A0ACD6B8J7 (Vibrio phage ICP1_2004_A) Explore A0ACD6B8J7  Go to UniProtKB:  A0ACD6B8J7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas1	D, E, G [auth d], H [auth e]	295	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00460
UniProt
Find proteins for A0ACD6B8J8 (Vibrio phage ICP1_2004_A) Explore A0ACD6B8J8  Go to UniProtKB:  A0ACD6B8J8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')	A [auth U]	21	Vibrio phage ICP1_2004_A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')	B [auth V]	21	Vibrio phage ICP1_2004_A

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 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: 2024-07-17 
Deposition Author(s): Zhang, L.X., Feng, Y.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32171274

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2025-07-16
  Changes: Data collection, Structure summary