8K29 | pdb_00008k29

ICP1 Csy-dsDNA complex (form 2)

• PDB DOI: https://doi.org/10.2210/pdb8K29/pdb
• NAKB: 8K29
• EM Map EMD-36835: 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: 3.18 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 9-mer - A6B1C1D1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 306.7 kDa 
• Atom Count: 21,055 
• Modeled Residue Count: 2,524 
• Deposited Residue Count: 2,558 
• Unique protein chains: 4
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy1	B [auth A]	179	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00450

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy2	C [auth B]	248	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00445

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy3	D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H]	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	J [auth I]	168	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00435

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (60-MER)	A [auth P]	60	Vibrio phage ICP1_2004_A

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (43-MER)	K [auth Q]	43	Vibrio phage ICP1_2004_A

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*TP*TP*CP*GP*TP*CP*AP*AP*CP*CP*CP*TP*TP*TP*GP*CP*TP*TP*AP*T)-3')	L [auth R]	24	Vibrio phage ICP1_2004_A

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 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: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-23
  Changes: Data collection