8K28 | pdb_00008k28

ICP1 Csy-dsDNA complex (form 1)

• PDB DOI: https://doi.org/10.2210/pdb8K28/pdb
• NAKB: 8K28
• EM Map EMD-36831: 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: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of csy complex with long DNA State1

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 304.13 kDa 
• Atom Count: 20,740 
• Modelled Residue Count: 2,516 
• Deposited Residue Count: 2,550 
• Unique protein chains: 4
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy1	A	179	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00450
UniProt
Find proteins for F1D5V8 (Vibrio phage ICP1_2004_A) Explore F1D5V8  Go to UniProtKB:  F1D5V8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy2	B	248	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00445
UniProt
Find proteins for F1D5V7 (Vibrio phage ICP1_2004_A) Explore F1D5V7  Go to UniProtKB:  F1D5V7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy3	C, D, E, F, G, L [auth H]	306	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00440
UniProt
Find proteins for F1D5V6 (Vibrio phage ICP1_2004_A) Explore F1D5V6  Go to UniProtKB:  F1D5V6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy4	H [auth I]	168	Vibrio phage ICP1_2004_A	Mutation(s): 0  Gene Names: TUST1-10_00435
UniProt
Find proteins for F1D5V5 (Vibrio phage ICP1_2004_A) Explore F1D5V5  Go to UniProtKB:  F1D5V5

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	I [auth Q]	33	Vibrio phage ICP1_2004_A

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	J [auth R]	27	Vibrio phage ICP1_2004_A

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (59-MER)	K [auth P]	59	Vibrio phage ICP1_2004_A

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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