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- PDB-7eu9: Crystal structure of the selenomethionine(SeMet)-derived Cas12i1 ... -

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Basic information

Entry
Database: PDB / ID: 7eu9
TitleCrystal structure of the selenomethionine(SeMet)-derived Cas12i1 R-loop complex before target DNA cleavage
Components
  • Cas12i1 D647A mutant
  • DNA (24-MER)
  • DNA (31-MER)
  • RNA (43-MER)
KeywordsRNA BINDING PROTEIN / Cas12i / Cas12i1 / CRISPR
Function / homologyCITRIC ACID / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsZhang, B. / Luo, D.Y. / Li, Y. / OuYang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770948 China
CitationJournal: Nat Commun / Year: 2021
Title: Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1.
Authors: Zhang, B. / Luo, D. / Li, Y. / Perculija, V. / Chen, J. / Lin, J. / Ye, Y. / Ouyang, S.
History
DepositionMay 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cas12i1 D647A mutant
B: RNA (43-MER)
C: DNA (31-MER)
D: DNA (24-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7155
Polymers166,5224
Non-polymers1921
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19330 Å2
ΔGint-117 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.064, 141.577, 208.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (31-MER)


Mass: 12326.935 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)
#4: DNA chain DNA (24-MER)


Mass: 12241.883 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Cas12i1 D647A mutant


Mass: 128172.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (43-MER)


Mass: 13781.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 80 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.6), 17% (w/v) Polyethylene glycol 3350, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→60 Å / Num. obs: 78375 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.4
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.969 / Num. unique obs: 11343 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
xia20.5.898data reduction
SCALA3.3.22data scaling
PHENIX1.13-2998phasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→58.63 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.487 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3923 5 %RANDOM
Rwork0.2276 ---
obs0.2297 74089 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 58.834 Å2 / Biso min: 27.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0 Å2
2--0.19 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 2.35→58.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8720 2037 13 79 10849
Biso mean--63.73 46.99 -
Num. residues----1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0189215
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.57415508
X-RAY DIFFRACTIONr_angle_other_deg1.0071.8321723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74651076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93723.105467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.803151624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1081548
X-RAY DIFFRACTIONr_chiral_restr0.0710.21473
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022101
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 269 -
Rwork0.298 5439 -
all-5708 -
obs--99.86 %

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