7KFU | pdb_00007kfu

Cas6-RT-Cas1--Cas2 complex

• PDB DOI: https://doi.org/10.2210/pdb7KFU/pdb
• EM Map EMD-22856: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Thiomicrospira sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-14 Released: 2021-03-31 
• Deposition Author(s): Hoel, C.M., Wang, J.Y., Doudna, J.A., Brohawn, S.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex.

Wang, J.Y., Hoel, C.M., Al-Shayeb, B., Banfield, J.F., Brohawn, S.G., Doudna, J.A.

(2021) Nat Commun 12: 2571-2571

• PubMed: 33958590 
• DOI: https://doi.org/10.1038/s41467-021-22900-y
• Primary Citation Related Structures: 
  7KFT, 7KFU


• PubMed Abstract: 
  

  CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1-Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 474.64 kDa 
• Atom Count: 21,848 
• Modeled Residue Count: 2,674 
• Deposited Residue Count: 4,134 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas2	A, B	99	Thiomicrospira sp.	Mutation(s): 0
UniProt
Find proteins for A0ACD6BA18 (Thiomicrospira sp. CG2_30_44_34) Explore A0ACD6BA18  Go to UniProtKB:  A0ACD6BA18

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas6-RT-Cas1	C, D, E, F	984	Thiomicrospira sp.	Mutation(s): 0
UniProt
Find proteins for A0ACD6BA19 (Thiomicrospira sp. CG2_30_44_34) Explore A0ACD6BA19  Go to UniProtKB:  A0ACD6BA19

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Hoel, C.M., Wang, J.Y., Doudna, J.A., Brohawn, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM123496

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2021-05-19
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references