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- PDB-2y8y: Structure B of CRISPR endoribonuclease Cse3 bound to 19 nt RNA -

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Basic information

Entry
Database: PDB / ID: 2y8y
TitleStructure B of CRISPR endoribonuclease Cse3 bound to 19 nt RNA
Components
  • 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*U)-3'
  • CSE3
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / FERREDOXIN-LIKE
Function / homology
Function and homology information


defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cse3
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsSashital, D.G. / Jinek, M. / Doudna, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: An RNA-Induced Conformational Change Required for Crispr RNA Cleavage by the Endoribonuclease Cse3.
Authors: Sashital, D.G. / Jinek, M. / Doudna, J.A.
History
DepositionFeb 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2022Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSE3
B: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*U)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19.9 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.280, 71.210, 76.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CSE3 / TTHB192


Mass: 24049.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PSV272 - HIS6-MBP-TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53WG9
#2: RNA chain 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*U)-3'


Mass: 6069.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA WITH 2'DEOXY MODIFICATION AT G 21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 5 / Details: 0.1 M SODIUM ACETATE, PH 5.0 4% PEG (W/V) 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11589 Å / Relative weight: 1
ReflectionResolution: 1.44→29 Å / Num. obs: 44574 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.56
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.29 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y8W

2y8w


Resolution: 1.44→33.752 Å / SU ML: 0.17 / σ(F): 2 / Phase error: 18.11 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 159-167 AND CHAIN B RESIDUE 13 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2054 1844 4.1 %
Rwork0.1845 --
obs0.1854 44574 99.99 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.297 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.4515 Å20 Å20 Å2
2--2.267 Å20 Å2
3----2.7185 Å2
Refinement stepCycle: LAST / Resolution: 1.44→33.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 401 0 351 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062074
X-RAY DIFFRACTIONf_angle_d1.0432898
X-RAY DIFFRACTIONf_dihedral_angle_d13.923854
X-RAY DIFFRACTIONf_chiral_restr0.069338
X-RAY DIFFRACTIONf_plane_restr0.005304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.49150.27751670.26714229X-RAY DIFFRACTION100
1.4915-1.55120.21371990.22184209X-RAY DIFFRACTION100
1.5512-1.62180.22061740.20124209X-RAY DIFFRACTION100
1.6218-1.70730.21561940.18644224X-RAY DIFFRACTION100
1.7073-1.81420.19871750.18174220X-RAY DIFFRACTION100
1.8142-1.95430.21021850.17374248X-RAY DIFFRACTION100
1.9543-2.1510.18891760.17474278X-RAY DIFFRACTION100
2.151-2.46210.20511870.17254297X-RAY DIFFRACTION100
2.4621-3.10170.21191890.18424310X-RAY DIFFRACTION100
3.1017-33.76090.19651980.1824506X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.93310.26790.22010.75870.16241.2743-0.0214-0.06430.1006-0.0041-0.05240.1023-0.0166-0.16320.07470.05480.0081-0.00110.0893-0.02450.0936-3.2202-2.06515.9434
20.97340.5549-0.60651.66-0.34661.0647-0.18360.4040.77840.35440.10630.0559-0.5308-0.0580.12370.36750.0615-0.03960.28310.14390.4278-8.77828.016-9.3145
30.81670.07890.22620.3487-0.02130.9908-0.02-0.04620.0432-0.0305-0.0017-0.0168-0.0784-0.01440.03250.0854-0.00590.00050.0766-0.01130.08232.4232-8.00785.9841
41.27930.48060.1751.1125-0.91.95010.00610.18820.305-0.08930.0677-0.0189-0.26370.1194-0.03630.1569-0.02530.03590.15960.0170.184910.29962.781-7.7505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:155)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 156:170)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 171:211)
4X-RAY DIFFRACTION4CHAIN B

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