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- PDB-7d8c: Crystal structure of the Cas12i1-crRNA binary complex -

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Basic information

Entry
Database: PDB / ID: 7d8c
TitleCrystal structure of the Cas12i1-crRNA binary complex
Components
  • 12i1
  • RNA (3-MER)
  • RNA (38-MER)
KeywordsRNA BINDING PROTEIN / The RNP Complex 3
Function / homologyCITRIC ACID / RNA / RNA (> 10)
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsZhang, B. / Luo, D.Y. / Li, Y. / OuYang, S.Y.
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
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 30, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 12i1
B: RNA (38-MER)
C: RNA (3-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4154
Polymers143,2223
Non-polymers1921
Water00
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)211.933, 211.933, 164.758
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein 12i1


Mass: 128216.500 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 (38-MER)


Mass: 14086.325 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)
#3: RNA chain RNA (3-MER)


Mass: 919.620 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)
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
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: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.2), 17% (w/v) Polyethylene glycol 3350, 2% Tacsimate (pH 4.0), 0.15 M sodium citrate tribasic dihydrate

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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: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.6→57.42 Å / Num. obs: 25821 / % possible obs: 99.9 % / Redundancy: 38.6 % / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 3.6→3.85 Å / Num. unique obs: 4599 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless0.7.1data scaling
PHENIX1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D2L

7d2l


Resolution: 3.6→57.42 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.88 / SU B: 55.123 / SU ML: 0.793 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.702 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3085 1290 5 %RANDOM
Rwork0.28 ---
obs0.2815 24504 99.85 %-
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: 144.549 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-5.58 Å22.79 Å20 Å2
2--5.58 Å2-0 Å2
3----18.09 Å2
Refinement stepCycle: final / Resolution: 3.6→57.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8557 871 13 0 9441
Biso mean--149.8 --
Num. residues----1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0149716
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178439
X-RAY DIFFRACTIONr_angle_refined_deg1.091.63113272
X-RAY DIFFRACTIONr_angle_other_deg0.8981.74219878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8451054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.03923.304454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg29.249151597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.6041544
X-RAY DIFFRACTIONr_chiral_restr0.0530.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021804
LS refinement shellResolution: 3.6→3.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 91 -
Rwork0.403 1764 -
all-1855 -
obs--99.89 %

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