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- PDB-8if0: NmeHNH-AcrIIC1 complex -

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Basic information

Entry
Database: PDB / ID: 8if0
TitleNmeHNH-AcrIIC1 complex
Components
  • Anti-CRISPR protein (AcrIIC1)
  • CRISPR-associated endonuclease Cas9
KeywordsSTRUCTURAL PROTEIN / complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
Anti-CRISPR protein (AcrIIC1) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsZhu, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200989 China
CitationJournal: To Be Published
Title: Inhibition Mechanism of CRISPR-Cas9 by Anti-CRISPR Protein AcrIIC1
Authors: Zhu, Y.L.
History
DepositionFeb 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: CRISPR-associated endonuclease Cas9
Y: Anti-CRISPR protein (AcrIIC1)


Theoretical massNumber of molelcules
Total (without water)28,7992
Polymers28,7992
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.061, 60.742, 46.428
Angle α, β, γ (deg.)90.000, 108.250, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11X-717-

HOH

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 19160.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9 / Production host: Escherichia coli (E. coli) / References: UniProt: X5EPV9
#2: Protein Anti-CRISPR protein (AcrIIC1)


Mass: 9637.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TCG3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M MES, pH 6.2, 26% PEG3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 34393 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.3
Reflection shellResolution: 1.57→1.61 Å / Rmerge(I) obs: 0.092 / Num. unique obs: 34393

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.57→50 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 --
Rwork0.193 --
obs-34393 99.7 %
Displacement parametersBiso mean: 40.82 Å2
Refinement stepCycle: LAST / Resolution: 1.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 0 140 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632010
X-RAY DIFFRACTIONf_angle_d0.73812694
X-RAY DIFFRACTIONf_chiral_restr0.0472265
X-RAY DIFFRACTIONf_plane_restr0.0039353
X-RAY DIFFRACTIONf_dihedral_angle_d22.9538784

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