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- PDB-7du0: Structure of an type I-F anti-crispr protein -

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Basic information

Entry
Database: PDB / ID: 7du0
TitleStructure of an type I-F anti-crispr protein
ComponentsAcrIF14
KeywordsVIRAL PROTEIN / monomer / two-domain
Function / homologyTail protein
Function and homology information
Biological speciesMoraxella phage Mcat5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsTeng, G. / Yue, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31822012 China
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR-Cas surveillance complex.
Authors: Xi Liu / Laixing Zhang / Yu Xiu / Teng Gao / Ling Huang / Yongchao Xie / Lingguang Yang / Wenhe Wang / Peiyi Wang / Yi Zhang / Maojun Yang / Yue Feng /
Abstract: CRISPR-Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of ...CRISPR-Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of both AcrIF14 and its complex with the crRNA-guided surveillance (Csy) complex. Our study demonstrates that apart from interacting with the Csy complex to block the hybridization of target DNA to the crRNA, AcrIF14 also endows the Csy complex with the ability to interact with non-sequence-specific dsDNA as AcrIF9 does. Further structural studies of the Csy-AcrIF14-dsDNA complex and biochemical studies uncover that the PAM recognition loop of the Cas8f subunit of the Csy complex and electropositive patches within the N-terminal domain of AcrIF14 are essential for the non-sequence-specific dsDNA binding to the Csy-AcrIF14 complex, which is different from the mechanism of AcrIF9. Our findings highlight the prevalence of Acr-induced non-specific DNA binding and shed light on future studies into the mechanisms of such Acr proteins.
History
DepositionJan 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: AcrIF14


Theoretical massNumber of molelcules
Total (without water)14,3681
Polymers14,3681
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.234, 34.929, 67.354
Angle α, β, γ (deg.)90.000, 118.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AcrIF14


Mass: 14368.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella phage Mcat5 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R6PCL0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 3350, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 17975 / % possible obs: 95.2 % / Redundancy: 5 % / CC1/2: 0.992 / Net I/σ(I): 24.5
Reflection shellResolution: 1.96→2.05 Å / Num. unique obs: 1782 / CC1/2: 0.655

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→29.91 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 859 4.78 %
Rwork0.2516 17116 -
obs0.2536 17975 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.2 Å2 / Biso mean: 44.0493 Å2 / Biso min: 21.24 Å2
Refinement stepCycle: final / Resolution: 1.96→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 0 40 1043
Biso mean---43.46 -
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-2.090.26461330.28952644277787
2.09-2.250.31881490.28252965311497
2.25-2.470.35421460.2953002314899
2.47-2.830.37421570.2842952310997
2.83-3.560.26981500.25632764291491
3.57-29.910.26471240.21832789291391

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