6NUD

Small conformation of ssRNA-bound CRISPR_Csm complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry.

Guo, M.Zhang, K.Zhu, Y.Pintilie, G.D.Guan, X.Li, S.Schmid, M.F.Ma, Z.Chiu, W.Huang, Z.

(2019) Cell Res 29: 305-312

  • DOI: 10.1038/s41422-019-0151-x
  • Primary Citation of Related Structures:  
    6NUE, 6NUD

  • PubMed Abstract: 
  • The type III CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated genes) systems are bacterially encoded adaptive immune systems for defense against invading nucleic acids. They accomplish this task through the coor ...

    The type III CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated genes) systems are bacterially encoded adaptive immune systems for defense against invading nucleic acids. They accomplish this task through the coordinated cleavage of invading substrates of single-stranded RNA and DNA (ssDNA and ssRNA) by the Csm (type III-A) or Cmr (type III-B) effector complexes. The ssRNA is complementarily bound to the CRISPR RNA (crRNA). However, the structural basis for the DNase and RNase activation of the Csm nucleoprotein complex is largely unknown. Here we report cryo-EM structures of the Csm-crRNA complex, with or without target ssRNA, at near-atomic resolution. Our cryo-EM maps allow us to build atomic models of the key macromolecular components, including Cas10, Csm2, Csm3, Csm4, crRNA and the invading ssRNA. Our structure resolves unambiguously the stoichiometry and tertiary structures of the Csm protein complex and the interactions between protein components and the crRNA/ssRNA. Interestingly, the new atomic structures of the Csm proteins presented here are similar to those of previously known Csm proteins in other species despite their low sequence similarity. Our combined structural and biochemical data suggest that ssRNA cleavage is preferentially carried out near its 5'-end, that the extent of interactions among the ssRNA, crRNA and the protein components regulates the DNase activity of the Csm complex, and that the 3' flanking sequence of ssRNA activates the Cas10 DNase activity allosterically.


    Organizational Affiliation

    HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China. huangzhiwei@hit.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm2ABM121Streptococcus thermophilusMutation(s): 0 
Gene Names: csm2
Find proteins for A0A0A7HIX1 (Streptococcus thermophilus)
Explore A0A0A7HIX1 
Go to UniProtKB:  A0A0A7HIX1
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR type III-associated RAMP protein Csm4I299Streptococcus thermophilusMutation(s): 0 
Gene Names: csm4CDA68_00841
Find proteins for A0A0A7HGA1 (Streptococcus thermophilus)
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Go to UniProtKB:  A0A0A7HGA1
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)J758Streptococcus thermophilusMutation(s): 0 
Gene Names: cas10csm1
EC: 3.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
Find proteins for A0A0A7HFE1 (Streptococcus thermophilus)
Explore A0A0A7HFE1 
Go to UniProtKB:  A0A0A7HFE1
Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR type III-associated RAMP protein Csm3CENOP220Streptococcus thermophilusMutation(s): 1 
Gene Names: csm3CDA68_00842
EC: 3.1
Find proteins for A0A0A7HIF0 (Streptococcus thermophilus)
Explore A0A0A7HIF0 
Go to UniProtKB:  A0A0A7HIF0
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
crRNAH72Streptococcus thermophilus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
target ssRNAU49Streptococcus thermophilus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
J
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP41GM103832
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesU54GM103297
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM079429
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10OD021600
National Natural Science Foundation of China (NSFC)China31825008
National Natural Science Foundation of China (NSFC)China31422014

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence