6KDV

Crystal structure of TtCas1-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of Cas1 in complex with branched DNA.

Yang, J.Li, J.Z.Wang, J.Y.Sheng, G.Wang, M.Zhao, H.T.Yang, Y.H.Wang, Y.L.

(2019) Sci China Life Sci --: --

  • DOI: 10.1007/s11427-019-9827-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cas1 is a key component of the CRISPR adaptation complex, which captures and integrates foreign DNA into the CRISPR array, resulting in the generation of new spacers. We have determined crystal structures of Thermus thermophilus Cas1 involved in new ...

    Cas1 is a key component of the CRISPR adaptation complex, which captures and integrates foreign DNA into the CRISPR array, resulting in the generation of new spacers. We have determined crystal structures of Thermus thermophilus Cas1 involved in new spacer acquisition both in complex with branched DNA and in the free state. Cas1 forms an asymmetric dimer without DNA. Conversely, two asymmetrical dimers bound to two branched DNAs result in the formation of a DNA-mediated tetramer, dimer of structurally asymmetrical dimers, in which the two subunits markedly present different conformations. In the DNA binding complex, the N-terminal domain adopts different orientations with respect to the C-terminal domain in the two monomers that form the dimer. Substrate binding triggers a conformational change in the loop 164-177 segment. This loop is also involved in the 3' fork arm and 5' fork arm strand recognition in monomer A and B, respectively. This study provides important insights into the molecular mechanism of new spacer adaptation.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. ylwang@ibp.ac.cn.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. ylwang@ibp.ac.cn.,Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,University of Chinese Academy of Sciences, Beijing, 100049, China. ylwang@ibp.ac.cn.,Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China. yanhuayang@126.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas1 2
B, A, D, C
325Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: cas1-2
EC: 3.1.-.-
Find proteins for Q53WG8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q53WG8
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')E,G23synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')F,H23synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 116.547α = 90.00
b = 201.199β = 90.00
c = 77.660γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31630015
National Natural Science Foundation of ChinaChina31725008

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release