8S36

DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state II)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference.

Cepaite, R.Klein, N.Miksys, A.Camara-Wilpert, S.Ragozius, V.Benz, F.Skorupskaite, A.Becker, H.Zvejyte, G.Steube, N.Hochberg, G.K.A.Randau, L.Pinilla-Redondo, R.Malinauskaite, L.Pausch, P.

(2024) Nat Commun 15: 9306-9306

  • DOI: https://doi.org/10.1038/s41467-024-53778-1
  • Primary Citation of Related Structures:  
    8RC2, 8RC3, 8RFJ, 8S35, 8S36, 8S37

  • PubMed Abstract: 

    CRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for gene regulation and plasmid competition. To understand how the type IV-A system associated effector complex achieves this interference, we determine cryo-EM structures of two evolutionarily distinct type IV-A complexes (types IV-A1 and IV-A3) bound to cognate DNA-targets in the presence and absence of the type IV-A signature DinG effector helicase. The structures reveal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form an R-loop structure. Additionally, we reveal differences between types IV-A1 and IV-A3 in DNA interactions and structural motifs that allow for in trans recruitment of DinG. Our study provides a detailed view of type IV-A mediated DNA-interference and presents a structural foundation for engineering type IV-A-based genome editing tools.


  • Organizational Affiliation

    LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR type AFERR-associated protein Csf2
A,
B,
C,
D,
E,
K [auth L]
350Klebsiella pneumoniaeMutation(s): 0 
Gene Names: AI2781V1_5179
UniProt
Find proteins for A0A333ESG5 (Klebsiella pneumoniae)
Explore A0A333ESG5 
Go to UniProtKB:  A0A333ESG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A333ESG5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR type AFERR-associated protein Csf3235Klebsiella pneumoniaeMutation(s): 0 
Gene Names: EAO17_29825
UniProt
Find proteins for A0A8G1XN67 (Klebsiella pneumoniae)
Explore A0A8G1XN67 
Go to UniProtKB:  A0A8G1XN67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8G1XN67
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR type AFERR-associated protein Csf1263Klebsiella pneumoniaeMutation(s): 0 
Gene Names: G4V31_29130
UniProt
Find proteins for A0A7Z7WW72 (Klebsiella pneumoniae)
Explore A0A7Z7WW72 
Go to UniProtKB:  A0A7Z7WW72
Entity Groups  
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UniProt GroupA0A7Z7WW72
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DEAD/DEAH box helicaseL [auth M]624Klebsiella pneumoniaeMutation(s): 0 
Gene Names: BL124_00021750
EC: 5.6.2.3
UniProt
Find proteins for A0A422ZM74 (Klebsiella pneumoniae)
Explore A0A422ZM74 
Go to UniProtKB:  A0A422ZM74
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UniProt GroupA0A422ZM74
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
crRNA61Klebsiella pneumoniae
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
TS-DNA60Klebsiella pneumoniae
Sequence Annotations
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  • Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
NTS-NDA60Klebsiella pneumoniae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth G]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government12-001-01-01-01
European Molecular Biology Organization (EMBO)European Union5342-2023
Other governmentS-MIP-22-10
Other governmentDFG-SPP2141

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release