8K22 | pdb_00008k22

ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (half form)

• PDB DOI: https://doi.org/10.2210/pdb8K22/pdb
• NAKB: 8K22
• EM Map EMD-36825: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/DNA/RNA
• 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of csy complex with long DNA State2

Zhang, L.X., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 15-mer - A6B4C1D1E1F1G1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - B4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 671.94 kDa 
• Atom Count: 39,285 
• Modeled Residue Count: 4,761 
• Deposited Residue Count: 5,668 
• Unique protein chains: 6
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy1	A [auth B]	178	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00450
UniProt
Find proteins for A0ACD6B8J6 (Vibrio phage ICP1_2004_A) Explore A0ACD6B8J6  Go to UniProtKB:  A0ACD6B8J6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy2	B [auth C]	248	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00445
UniProt
Find proteins for A0ACD6B8J5 (Vibrio phage ICP1_2004_A) Explore A0ACD6B8J5  Go to UniProtKB:  A0ACD6B8J5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas1	C [auth D], D [auth E], P [auth d], Q [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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy3	E [auth G], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M]	306	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00440
UniProt
Find proteins for A0ACD6B8J4 (Vibrio phage ICP1_2004_A) Explore A0ACD6B8J4  Go to UniProtKB:  A0ACD6B8J4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy4	F [auth H]	168	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00435
UniProt
Find proteins for A0ACD6B8J3 (Vibrio phage ICP1_2004_A) Explore A0ACD6B8J3  Go to UniProtKB:  A0ACD6B8J3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
HD Cas3-type domain-containing protein	O [auth a], R [auth A]	930	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: 6
Molecule	Chains	Length	Organism	Image
RNA (60-MER)	L [auth P]	60	Vibrio phage ICP1_2004_A

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (43-MER)	M [auth Q], S [auth U]	43	Vibrio phage ICP1_2004_A

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	N [auth R]	31	Vibrio phage ICP1_2004_A

Entity ID: 10
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')	T [auth V]	21	Vibrio phage ICP1_2004_A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	U [auth A], V [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 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.

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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: 2025-07-23
  Changes: Data collection, Structure summary