6NE0

Structure of double-stranded target DNA engaged Csy complex from Pseudomonas aeruginosa (PA-14)

• PDB DOI:  https://doi.org/10.2210/pdb6NE0/pdb
• Entry: 6NE0 supersedes: 6MPU
• EM Map EMD-9191: EMDB EMDataResource
• NAKB: 6NE0

• Classification: IMMUNE SYSTEM/RNA
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-15 Released: 2018-12-26 
• Deposition Author(s): Chowdhury, S., Rollins, M.F., Carter, J., Golden, S.M., Miettinen, H.M., Santiago-Frangos, A., Faith, D., Lawrence, M.C., Wiedenheft, B., Lander, G.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry.

Rollins, M.F., Chowdhury, S., Carter, J., Golden, S.M., Miettinen, H.M., Santiago-Frangos, A., Faith, D., Lawrence, C.M., Lander, G.C., Wiedenheft, B.

(2019) Mol Cell 74: 132-142.e5

• PubMed: 30872121 
• DOI: https://doi.org/10.1016/j.molcel.2019.02.001
• Primary Citation of Related Structures:  
  6NE0


• PubMed Abstract: 
  

Bacteria and archaea have evolved sophisticated adaptive immune systems that rely on CRISPR RNA (crRNA)-guided detection and nuclease-mediated elimination of invading nucleic acids. Here, we present the cryo-electron microscopy (cryo-EM) structure of the type I-F crRNA-guided surveillance complex (Csy complex) from Pseudomonas aeruginosa bound to a double-stranded DNA target. Comparison of this structure to previously determined structures of this complex reveals a ∼180-degree rotation of the C-terminal helical bundle on the "large" Cas8f subunit. We show that the double-stranded DNA (dsDNA)-induced conformational change in Cas8f exposes a Cas2/3 "nuclease recruitment helix" that is structurally homologous to a virally encoded anti-CRISPR protein (AcrIF3). Structural homology between Cas8f and AcrIF3 suggests that AcrIF3 is a mimic of the Cas8f nuclease recruitment helix.

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Organizational Affiliation: 

Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A6B1C1D1 Local Symmetry: Helical - H  (3D View)
Local Stoichiometry: Homo 6-mer - A6 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 375.92 kDa 
• Atom Count: 24,044 
• Modelled Residue Count: 2,979 
• Deposited Residue Count: 3,140 
• Unique protein chains: 4
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Csy1	A	434	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: csy1, PA14_33330
UniProt
Find proteins for Q02ML9 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02ML9  Go to UniProtKB:  Q02ML9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Csy2	B	327	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: csy2, PA14_33320
UniProt
Find proteins for Q02MM0 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02MM0  Go to UniProtKB:  Q02MM0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Csy3	C, D, E, F, G, H	342	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: csy3, csy1-3, PA14_33310
UniProt
Find proteins for Q02MM1 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02MM1  Go to UniProtKB:  Q02MM1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas6/Csy4	I [auth L]	189	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: cas6f, csy4, PA14_33300 EC: 3.1
UniProt
Find proteins for Q02MM2 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02MM2  Go to UniProtKB:  Q02MM2

Entity ID: 5
Molecule	Chains	Length	Organism	Image
CRISPR RNA (60-MER)	J [auth M]	60	Pseudomonas aeruginosa UCBPP-PA14

Entity ID: 6
Molecule	Chains	Length	Organism	Image
CRISPR target DNA (44-MER)	K [auth N]	44	Pseudomonas aeruginosa UCBPP-PA14

Entity ID: 7
Molecule	Chains	Length	Organism	Image
Non-complementary R-loop DNA strand	L [auth O]	34	Pseudomonas aeruginosa UCBPP-PA14

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Chowdhury, S., Rollins, M.F., Carter, J., Golden, S.M., Miettinen, H.M., Santiago-Frangos, A., Faith, D., Lawrence, M.C., Wiedenheft, B., Lander, G.C.
• This entry supersedes: 6MPU

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2EB020402, P20GM103500, P30GM110732, R01GM110270, R01GM108888,R21AI130670
National Science Foundation (NSF, United States)	United States	EPS-110134

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Structure summary
• Version 1.2: 2019-03-20
  Changes: Data collection, Database references
• Version 1.3: 2019-03-27
  Changes: Data collection, Database references
• Version 1.4: 2019-04-17
  Changes: Data collection, Database references
• Version 1.5: 2019-11-27
  Changes: Author supporting evidence
• Version 1.6: 2019-12-25
  Changes: Database references