6VBW | pdb_00006vbw

Cryo-EM structure of Cascade-TniQ-dsDNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb6VBW/pdb
• EM Map EMD-21146: EMDB EMDataResource
• NAKB: 6VBW

• Classification: IMMUNE SYSTEM
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-19 Released: 2020-01-29 
• Deposition Author(s): Jia, N., Patel, D.J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-function insights into the initial step of DNA integration by a CRISPR-Cas-Transposon complex.

Jia, N., Xie, W., de la Cruz, M.J., Eng, E.T., Patel, D.J.

(2020) Cell Res 30: 182-184

• PubMed: 31925391 
• DOI: https://doi.org/10.1038/s41422-019-0272-2
• Primary Citation of Related Structures:  
  6V9P, 6V9Q, 6VBW

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Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. [e-mail].
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A6B2C1D1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 483.35 kDa 
• Atom Count: 29,087 
• Modeled Residue Count: 3,450 
• Deposited Residue Count: 3,922 
• Unique protein chains: 4
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas8	D [auth A]	640	Vibrio cholerae	Mutation(s): 0
UniProt
Find proteins for A0A6I8WFX4 (Vibrio cholerae) Explore A0A6I8WFX4  Go to UniProtKB:  A0A6I8WFX4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas7	E [auth B], F [auth C], G [auth D], H [auth F], I [auth E], J [auth G]	352	Vibrio cholerae	Mutation(s): 0
UniProt
Find proteins for A0A6I8WFX5 (Vibrio cholerae) Explore A0A6I8WFX5  Go to UniProtKB:  A0A6I8WFX5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas6	K [auth H]	199	Vibrio cholerae	Mutation(s): 0
UniProt
Find proteins for A0A6I8WFX3 (Vibrio cholerae) Explore A0A6I8WFX3  Go to UniProtKB:  A0A6I8WFX3

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
TniQ	L [auth I], M [auth J]	394	Vibrio cholerae	Mutation(s): 0
UniProt
Find proteins for A0A6I8WFX7 (Vibrio cholerae) Explore A0A6I8WFX7  Go to UniProtKB:  A0A6I8WFX7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*CP*AP*CP*CP*AP*AP*TP*TP*TP*AP*TP*TP*TP*A)-3')	A [auth M]	22	Vibrio cholerae

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (100-MER)	B [auth L]	100	Vibrio cholerae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (61-MER)	C [auth K]	61	Vibrio cholerae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	N [auth I], O [auth I], P [auth J], Q [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Jia, N., Patel, D.J.

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references