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- PDB-6lu0: Crystal structure of Cas12i2 ternary complex with 12 nt spacer -

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Basic information

Entry
Database: PDB / ID: 6lu0
TitleCrystal structure of Cas12i2 ternary complex with 12 nt spacer
Components
  • Cas12i2
  • DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3')
  • DNA (5'-D(*GP*CP*TP*TP*GP*CP*TP*CP*TP*GP*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*C)-3')
  • crRNA
KeywordsHYDROLASE/RNA/DNA / CRISPR-Cas / Cas12i2 / Cas12i2 binary complex / HYDROLASE / HYDROLASE-RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsHuang, X. / Sun, W. / Cheng, Z. / Chen, M. / Li, X. / Wang, J. / Sheng, G. / Gong, W. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630015 China
National Natural Science Foundation of China (NSFC)31725008 China
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2.
Authors: Huang, X. / Sun, W. / Cheng, Z. / Chen, M. / Li, X. / Wang, J. / Sheng, G. / Gong, W. / Wang, Y.
History
DepositionJan 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas12i2
B: crRNA
D: DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3')
C: DNA (5'-D(*GP*CP*TP*TP*GP*CP*TP*CP*TP*GP*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)149,8834
Polymers149,8834
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-75 kcal/mol
Surface area50690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.553, 122.672, 284.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Cas12i2


Mass: 121411.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: RNA chain crRNA


Mass: 18710.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3')


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*CP*TP*TP*GP*CP*TP*CP*TP*GP*TP*TP*GP*AP*AP*AP*GP*CP*GP*GP*C)-3')


Mass: 6470.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.8
Details: 0.2 M NaCl, 0.1 M Bis-Tris propane pH 7.8, 18.5% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26456 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 63.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Χ2: 0.933 / Net I/σ(I): 26.5
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 4 / Num. unique obs: 1247 / CC1/2: 0.853 / Rpim(I) all: 0.368 / Rrim(I) all: 0.94 / Χ2: 0.93 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LTR

6ltr


Resolution: 3.22→29.56 Å / SU ML: 0.3588 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 1339 5.1 %
Rwork0.2069 24921 -
obs0.2082 26260 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.81 Å2
Refinement stepCycle: LAST / Resolution: 3.22→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7448 1206 44 21 8719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00428988
X-RAY DIFFRACTIONf_angle_d0.794412409
X-RAY DIFFRACTIONf_chiral_restr0.0491401
X-RAY DIFFRACTIONf_plane_restr0.00551379
X-RAY DIFFRACTIONf_dihedral_angle_d19.8361671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.340.30951180.26231982X-RAY DIFFRACTION79.37
3.34-3.470.27581390.24242465X-RAY DIFFRACTION98.9
3.47-3.630.2589940.24072532X-RAY DIFFRACTION99.02
3.63-3.820.2551420.22332508X-RAY DIFFRACTION99.74
3.82-4.060.24821490.19972551X-RAY DIFFRACTION99.85
4.06-4.370.21321200.19032527X-RAY DIFFRACTION99.96
4.37-4.810.1861360.17942555X-RAY DIFFRACTION99.74
4.81-5.50.26191440.19022569X-RAY DIFFRACTION99.85
5.5-6.910.20871560.21082556X-RAY DIFFRACTION99.89
6.91-29.560.19951410.20072676X-RAY DIFFRACTION99.37

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