8K23 | pdb_00008k23

ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry

• PDB DOI: https://doi.org/10.2210/pdb8K23/pdb
• NAKB: 8K23
• EM Map EMD-36826: 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: 3.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry

Zhang, L.X., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B4C2D2E2F2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 983.71 kDa 
• Atom Count: 67,168 
• Modeled Residue Count: 8,150 
• Deposited Residue Count: 8,258 
• Unique protein chains: 6
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy1	A [auth B], S [auth b]	177	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00450

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy2	B [auth C], T [auth c]	248	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00445

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas1	C [auth D], D [auth E], U [auth d], V [auth e]	302	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00460

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy3	AA [auth k], BA [auth l], CA [auth m], E [auth G], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], W [auth g], Y [auth i], Z [auth j]	306	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00440

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy4	F [auth H], X [auth h]	168	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00435

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

Entity ID: 6
Molecule	Chains	Length	Organism	Image
RNA (60-MER)	DA [auth p], L [auth P]	60	Vibrio phage ICP1_2004_A

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

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	FA [auth r], 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')	Q [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)	GA [auth A], HA [auth A], IA [auth a], JA [auth a]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.75 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