5DQZ

Crystal Structure of Cas-DNA-PAM complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems.

Wang, J., Li, J., Zhao, H., Sheng, G., Wang, M., Yin, M., Wang, Y.

(2015) Cell 163: 840-853

  • DOI: https://doi.org/10.1016/j.cell.2015.10.008
  • Primary Citation of Related Structures:  
    5DLJ, 5DQT, 5DQU, 5DQZ

  • PubMed Abstract: 

    • Bacteria acquire memory of viral invaders by incorporating invasive DNA sequence elements into the host CRISPR locus, generating a new spacer within the CRISPR array. We report on the structures of Cas1-Cas2-dual-forked DNA complexes in an effort toward understanding how the protospacer is sampled prior to insertion into the CRISPR locus ...

    Bacteria acquire memory of viral invaders by incorporating invasive DNA sequence elements into the host CRISPR locus, generating a new spacer within the CRISPR array. We report on the structures of Cas1-Cas2-dual-forked DNA complexes in an effort toward understanding how the protospacer is sampled prior to insertion into the CRISPR locus. Our study reveals a protospacer DNA comprising a 23-bp duplex bracketed by tyrosine residues, together with anchored flanking 3' overhang segments. The PAM-complementary sequence in the 3' overhang is recognized by the Cas1a catalytic subunits in a base-specific manner, and subsequent cleavage at positions 5 nt from the duplex boundary generates a 33-nt DNA intermediate that is incorporated into the CRISPR array via a cut-and-paste mechanism. Upon protospacer binding, Cas1-Cas2 undergoes a significant conformational change, generating a flat surface conducive to proper protospacer recognition. Here, our study provides important structure-based mechanistic insights into PAM-dependent spacer acquisition.

    Organizational Affiliation: 

    Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: ylwang@ibp.ac.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1A [auth D],
B [auth C],
C [auth A],
D [auth B]		305Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbT, cas1, b2755, JW2725
EC: 3.1
UniProt
Find proteins for Q46896 (Escherichia coli (strain K12))
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Go to UniProtKB:  Q46896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46896
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas2G [auth F],
H [auth E]		94Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbF, cas2, b2754, JW5438
EC: 3.1
UniProt
Find proteins for P45956 (Escherichia coli (strain K12))
Explore P45956 
Go to UniProtKB:  P45956
Entity Groups  
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UniProt GroupP45956
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (36-MER)E [auth G]36Escherichia coli
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (36-MER)F [auth H]36Escherichia coli
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
I [auth C],
J [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.771α = 90
b = 193.38β = 90
c = 193.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data processing
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references