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- PDB-2y9h: Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA -

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Basic information

Entry
Database: PDB / ID: 2y9h
TitleStructure A 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*UP)-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: 2.5 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 14, 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

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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*UP)-3'
C: CSE3
D: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
E: CSE3
F: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
G: CSE3
H: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
I: CSE3
J: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
K: CSE3
L: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
M: CSE3
N: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
O: CSE3
P: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)240,95716
Polymers240,95716
Non-polymers00
Water8,557475
1
A: CSE3
B: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-21.8 kcal/mol
Surface area13890 Å2
MethodPISA
2
C: CSE3
D: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-22.1 kcal/mol
Surface area13690 Å2
MethodPISA
3
E: CSE3
F: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-22 kcal/mol
Surface area13880 Å2
MethodPISA
4
G: CSE3
H: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-22.7 kcal/mol
Surface area12740 Å2
MethodPISA
5
I: CSE3
J: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-19.6 kcal/mol
Surface area12730 Å2
MethodPISA
6
K: CSE3
L: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-17.3 kcal/mol
Surface area12570 Å2
MethodPISA
7
M: CSE3
N: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18.6 kcal/mol
Surface area12240 Å2
MethodPISA
8
O: CSE3
P: 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)30,1202
Polymers30,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-11.7 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.860, 149.810, 87.260
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CSE3 / TTHB192


Mass: 24049.973 Da / Num. of mol.: 8
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*UP)-3'


Mass: 6069.650 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: RNA WITH 2'DEOXY MODIFICATION AT G 21
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.2 / Details: 0.1 M MES, PH 6.2, 8% PEG (W/V) 10000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999963
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999963 Å / Relative weight: 1
ReflectionResolution: 2.5→58.7 Å / Num. obs: 75718 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 46.27 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.84
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.14 / % possible all: 99.8

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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: 2.5→58.697 Å / SU ML: 0.49 / σ(F): 1.99 / Phase error: 36.15 / Stereochemistry target values: ML
Details: CHAIN E RESIDUES 160-161 ARE DISORDERED. CHAIN G RESIDUES 51-55 AND 159-166 ARE DISORDERED. CHAIN I RESIDUES 52-54, 74, 140-141 AND 156- 167 ARE DISORDERED. CHAIN K RESIDUES 52-54, 140-143 ...Details: CHAIN E RESIDUES 160-161 ARE DISORDERED. CHAIN G RESIDUES 51-55 AND 159-166 ARE DISORDERED. CHAIN I RESIDUES 52-54, 74, 140-141 AND 156- 167 ARE DISORDERED. CHAIN K RESIDUES 52-54, 140-143 AND 156-169 ARE DISORDERED. CHAIN M RESIDUES 51-55, 140-142 AND 157-168 ARE DISORDERED. CHAIN O RESIDUES 51-55, 71- 75, 138-143 AND 154-172 ARE DISORDERED. SIDE CHAINS FOR CHAIN O WERE OMITTED DUE TO HIGH DEGREES OF DISORDER THROUGHOUT THE MOLECULE. PHOSPHATE BETWEEN A22 AND U23 IS PRESENT FOR CHAINS B, D, F, H, J AND L, AND REST OF U23 IS DISORDERED FOR ALL RNA CHAINS.
RfactorNum. reflection% reflection
Rfree0.2895 1761 2.3 %
Rwork0.2305 --
obs0.232 75718 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.777 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.6493 Å20 Å2-2.7582 Å2
2---2.0188 Å20 Å2
3---0.3695 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12116 3072 0 475 15663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915787
X-RAY DIFFRACTIONf_angle_d1.21522096
X-RAY DIFFRACTIONf_dihedral_angle_d15.9276367
X-RAY DIFFRACTIONf_chiral_restr0.072593
X-RAY DIFFRACTIONf_plane_restr0.0072341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.42631770.33397355X-RAY DIFFRACTION100
2.5894-2.6930.40621800.31217384X-RAY DIFFRACTION100
2.693-2.81560.39211770.29527397X-RAY DIFFRACTION100
2.8156-2.9640.30971540.26077389X-RAY DIFFRACTION100
2.964-3.14970.3371850.23487385X-RAY DIFFRACTION100
3.1497-3.39290.28111700.22227424X-RAY DIFFRACTION100
3.3929-3.73430.28781880.22647386X-RAY DIFFRACTION100
3.7343-4.27450.27771680.20417417X-RAY DIFFRACTION100
4.2745-5.38490.22811850.18617425X-RAY DIFFRACTION100
5.3849-58.71270.24211770.22127395X-RAY DIFFRACTION98
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)
10.0418-0.3083-0.1880.6820.11740.01470.1062-0.0746-0.15120.0475-0.1855-0.1226-0.02240.007-0.00260.1455-0.003-0.05990.12190.12060.2667-37.5827-15.623537.6104
21.11990.84830.01931.1438-0.44761.44570.3299-0.7401-0.57710.4726-0.337-0.6687-0.111-0.00250.12320.316-0.178-0.14340.41280.33140.3771-37.9345-11.343256.8063
30.28320.55720.30961.54010.21850.33910.1844-0.0369-0.0859-0.1333-0.31180.1090.0027-0.0352-0.02410.14330.0639-0.09230.0803-0.04140.1484-48.4046-51.5125-7.2607
40.97820.04270.44581.4577-0.27390.94590.26710.07870.1309-0.1764-0.3216-0.81110.22380.26030.06710.09270.0229-0.00570.16030.13560.5034-28.8867-49.7441-6.0596
51.188-0.81870.06461.22150.22280.14760.10710.24810.2103-0.1287-0.3106-0.34340.00260.0120.0570.10230.05680.03260.13440.10630.1354-33.6734-14.4935-5.5918
60.6910.5020.10230.6878-0.17250.2102-0.06220.2724-0.00480.1113-0.04330.1522-0.1316-0.1030.00180.28140.0444-0.05150.1386-0.03780.1203-34.4004-10.562213.7537
70.366-0.4570.06131.3687-0.44270.45020.10760.00340.0115-0.0283-0.2199-0.0929-0.0017-0.00120.07380.13920.0085-0.09270.13410.0240.1475-52.2247-51.423235.8596
80.0311-0.0096-0.08031.4340.48620.8699-0.09810.05650.1498-0.0041-0.0779-1.0845-0.09650.4430.20820.1001-0.0048-0.11780.24250.21490.5961-32.4624-50.467637.1035
91.1491-0.44930.10350.0670.10240.541-0.0793-0.0307-0.0696-0.00440.08590.14240.13270.0313-0.00240.14140.038-0.03310.0638-0.00080.13153.0466-34.04948.6026
100.65-0.5247-0.16560.5107-0.29050.63310.3032-0.0811-0.099-0.3109-0.0950.0813-0.07350.1828-0.09940.20080.0378-0.01920.2781-0.0190.06098.6394-34.296928.8641
110.5888-0.002-0.01881.2636-0.19020.45130.00170.11610.0541-0.09280.0410.216-0.07190.1304-0.04890.15880.05990.00240.0953-0.00050.09956.421-33.81475.3098
122.7415-0.6478-1.41180.44030.57030.98720.34620.3243-0.127-0.09350.04780.203-0.4507-0.2613-0.31380.22420.20520.02840.4740.1020.102412.3055-33.5759-14.6646
130.78410.0828-0.48191.1007-0.19460.3212-0.13-0.05740.0741-0.22780.14990.12060.0554-0.0760.0690.11490.0026-0.04770.09860.010.0859-7.7712-75.783314.9921
140.40170.5414-0.07170.6202-0.14790.27610.1013-0.16660.17760.0024-0.07080.6276-0.38760.0569-0.03350.3364-0.0598-0.03290.2066-0.01990.4974-1.5298-57.494420.3696
150.6071-0.0666-0.59450.2540.08361.34610.1723-0.09050.35470.40070.4884-0.1256-0.0557-0.163-0.43061.0667-0.0934-0.5190.22630.04430.92863.5646-1.283628.3898
160.2812-0.81870.10122.6717-0.10690.16870.05370.33020.18040.78340.31860.3905-0.1263-0.152-0.18461.06630.2913-0.43620.86730.35081.9572-2.021617.470623.1418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P

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