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 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Cas1 in complex with branched DNA.

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

(2020) Sci China Life Sci 63: 516-528

  • DOI: https://doi.org/10.1007/s11427-019-9827-x
  • Primary Citation of Related Structures:  
    6KDV, 6KE1

  • 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 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

    Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1 2A [auth B],
B [auth A],
C [auth D],
D [auth C]
325Thermus thermophilus HB8Mutation(s): 0 
Gene Names: cas1-2TTHB193
EC: 3.1
UniProt
Find proteins for Q53WG8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53WG8 
Go to UniProtKB:  Q53WG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53WG8
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
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, G
23synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
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, H
23synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth B],
B [auth A],
C [auth D],
D [auth C]
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 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.547α = 90
b = 201.199β = 90
c = 77.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references