8ZP7

Cryo-EM structure of Cas5-HNH Cascade bound with sDNA, Conf1

• PDB DOI: https://doi.org/10.2210/pdb8ZP7/pdb
• NAKB: 8ZP7
• EM Map EMD-60328: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli, Candidatus Cloacimonetes bacterium ADurb.Bin088
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-29 Released: 2024-12-04 
• Deposition Author(s): Liu, Y.N., Wang, L., Zhang, H., Zhu, H.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Cas5-HNH Cascade bound with sDNA, Conf1

Liu, Y.N., Wang, L., Zhang, H., Zhu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A5B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B1C1D1E1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 446.23 kDa 
• Atom Count: 27,540 
• Modelled Residue Count: 3,395 
• Deposited Residue Count: 3,769 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Cse1 (CRISPR_cse1)	B [auth C]	546	Candidatus Cloacimonetes bacterium ADurb.Bin088	Mutation(s): 0  Gene Names: BWX75_00747
UniProt
Find proteins for A0A1V6F8D1 (Candidatus Cloacimonetes bacterium ADurb.Bin088) Explore A0A1V6F8D1  Go to UniProtKB:  A0A1V6F8D1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Cse2 (CRISPR_cse2)	C [auth E]	174	Candidatus Cloacimonetes bacterium ADurb.Bin088	Mutation(s): 0  Gene Names: BWX75_00748
UniProt
Find proteins for A0A1V6F8C9 (Candidatus Cloacimonetes bacterium ADurb.Bin088) Explore A0A1V6F8C9  Go to UniProtKB:  A0A1V6F8C9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cascade subunit CasC	D [auth F], E [auth H], F [auth I], G [auth J], H [auth K], I [auth G]	378	Candidatus Cloacimonetes bacterium ADurb.Bin088	Mutation(s): 0  Gene Names: casC, BWX75_00749
UniProt
Find proteins for A0A1V6F8B5 (Candidatus Cloacimonetes bacterium ADurb.Bin088) Explore A0A1V6F8B5  Go to UniProtKB:  A0A1V6F8B5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cascade subunit CasD	J [auth B]	388	Candidatus Cloacimonetes bacterium ADurb.Bin088	Mutation(s): 0  Gene Names: casD, BWX75_00750
UniProt
Find proteins for A0A1V6F8C5 (Candidatus Cloacimonetes bacterium ADurb.Bin088) Explore A0A1V6F8C5  Go to UniProtKB:  A0A1V6F8C5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cse3	K [auth D]	272	Candidatus Cloacimonetes bacterium ADurb.Bin088	Mutation(s): 0  Gene Names: cse3, BWX75_00751 EC: 3.1
UniProt
Find proteins for A0A1V6F8C4 (Candidatus Cloacimonetes bacterium ADurb.Bin088) Explore A0A1V6F8C4  Go to UniProtKB:  A0A1V6F8C4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (61-MER)	A	61	Escherichia coli

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (60-MER)	L [auth M]	60	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	M [auth C], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Liu, Y.N., Wang, L., Zhang, H., Zhu, H.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release