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- PDB-9jxx: Crystal structure of SiRe_0806 in complex with cA4 -

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Basic information

Entry
Database: PDB / ID: 9jxx
TitleCrystal structure of SiRe_0806 in complex with cA4
Components
  • PIN domain-containing protein
  • RNA (5'-R(P*AP*AP*AP*A)-3')
KeywordsIMMUNE SYSTEM/RNA / Sulfolobus islandicus / SiRe_0806 / cyclic oligo-adenylates (cOAs) / CARF domain / PIN domain / RNase / IMMUNE SYSTEM-RNA complex
Function / homologyRNA / PIN domain-containing protein
Function and homology information
Biological speciesSaccharolobus islandicus REY15A (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, F. / Zhao, P. / Bi, X. / She, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0906800 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Cyclic tetraadenylate binding induces dimerization of protein dimers to activate a CRISPR-associated PIN nuclease.
Authors: Wang, F. / Zhao, P. / Bi, X. / Zheng, R. / Tian, X. / Xu, J. / Jiang, S. / Li, G. / Shen, Y. / She, Q.
History
DepositionOct 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PIN domain-containing protein
D: PIN domain-containing protein
Y: RNA (5'-R(P*AP*AP*AP*A)-3')
A: PIN domain-containing protein
C: PIN domain-containing protein
X: RNA (5'-R(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)200,5466
Polymers200,5466
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18020 Å2
ΔGint-22 kcal/mol
Surface area65740 Å2
MethodPISA
2
B: PIN domain-containing protein
D: PIN domain-containing protein
Y: RNA (5'-R(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)100,2733
Polymers100,2733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-10 kcal/mol
Surface area35580 Å2
MethodPISA
3
A: PIN domain-containing protein
C: PIN domain-containing protein
X: RNA (5'-R(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)100,2733
Polymers100,2733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-10 kcal/mol
Surface area35490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.468, 81.839, 86.217
Angle α, β, γ (deg.)75.47, 87.09, 61.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PIN domain-containing protein


Mass: 49500.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Author remarks: Amino acids 1-417 correspond to the SiRe_0806 protein (UNP F0NH84), amino acids 418-423 constitute the linker connecting the SiRe_0806 protein to the C-terminal His-tag, and ...Details: Author remarks: Amino acids 1-417 correspond to the SiRe_0806 protein (UNP F0NH84), amino acids 418-423 constitute the linker connecting the SiRe_0806 protein to the C-terminal His-tag, and amino acids 424-429 represent the His-tag.
Source: (gene. exp.) Saccharolobus islandicus REY15A (archaea)
Strain: REY15A / Gene: SiRe_0806 / Production host: Saccharolobus islandicus REY15A (archaea) / References: UniProt: F0NH84
#2: RNA chain RNA (5'-R(P*AP*AP*AP*A)-3')


Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH=8.0; 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→48.82 Å / Num. obs: 58836 / % possible obs: 92.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.361 / Num. unique obs: 4703

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.82 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 2897 4.93 %
Rwork0.2062 --
obs0.2082 58808 92.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13410 176 0 76 13662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213823
X-RAY DIFFRACTIONf_angle_d0.54218675
X-RAY DIFFRACTIONf_dihedral_angle_d7.6961932
X-RAY DIFFRACTIONf_chiral_restr0.0422123
X-RAY DIFFRACTIONf_plane_restr0.0042356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.32521380.31472746X-RAY DIFFRACTION94
2.54-2.580.36381510.29562654X-RAY DIFFRACTION94
2.58-2.630.31831150.28752730X-RAY DIFFRACTION94
2.63-2.680.2761410.27742620X-RAY DIFFRACTION92
2.68-2.740.30851170.26082614X-RAY DIFFRACTION89
2.74-2.80.33751170.24492346X-RAY DIFFRACTION82
2.8-2.860.29331330.24372795X-RAY DIFFRACTION96
2.86-2.930.27221380.24842804X-RAY DIFFRACTION96
2.93-3.010.3021550.25892707X-RAY DIFFRACTION96
3.01-3.10.33871630.26632719X-RAY DIFFRACTION96
3.1-3.20.30951480.25162728X-RAY DIFFRACTION95
3.2-3.320.27241450.22352712X-RAY DIFFRACTION94
3.32-3.450.30091460.2222649X-RAY DIFFRACTION93
3.45-3.610.27651270.22392445X-RAY DIFFRACTION86
3.61-3.80.23611140.21732701X-RAY DIFFRACTION92
3.8-4.030.23911510.19062743X-RAY DIFFRACTION96
4.03-4.340.24081180.17552771X-RAY DIFFRACTION95
4.34-4.780.2321150.16542708X-RAY DIFFRACTION93
4.78-5.470.18521290.17652489X-RAY DIFFRACTION87
5.47-6.890.2431850.20442694X-RAY DIFFRACTION96
6.89-48.820.15531510.15452536X-RAY DIFFRACTION89
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)
10.2669-0.1821-0.17520.62030.16010.1182-0.05690.1360.0681-0.4175-0.0861-0.203-0.29030.2405-0.02540.6143-0.20370.15250.68470.04050.383616.70329.334-27.7655
20.62530.6003-0.38090.5731-0.71391.0404-0.08340.1010.17020.05280.10560.2526-0.1532-0.0165-0.00610.3481-0.0534-0.04690.275-0.0040.3763-10.993228.6424-7.1083
30.45460.3443-0.26550.7574-0.2320.22390.0766-0.0969-0.2757-0.666-0.0961-0.30690.11260.15370.20940.21430.06990.27990.4701-0.010.371411.65182.3365-21.7425
40.4695-0.32350.10450.2354-0.08360.06540.05550.022-0.2179-0.22930.0350.1188-0.3057-0.15190.01080.4589-0.0506-0.02240.3387-0.02560.3046-23.5023-0.8912-18.3178
50.73860.1796-0.08130.2503-0.25190.2823-0.1298-0.029-0.1844-0.1875-0.0026-0.0596-0.18380.0098-0.00020.49420.06310.03150.4073-0.01220.3557-10.2505-5.2079-23.7363
60.02440.02270.02290.02130.01920.0148-0.22910.00190.2793-0.3048-0.10070.00580.2250.35860.00010.653-0.07230.03570.66340.02830.492213.631917.0119-21.5145
70.38480.2613-0.04720.64580.13810.2953-0.1677-0.0907-0.10480.43620.0216-0.26360.17470.062-0.00410.53020.1679-0.13410.50760.02760.429217.8603-29.42827.775
80.8106-0.92620.48520.6269-0.58480.9293-0.0433-0.0834-0.2355-0.11240.10970.26680.14130.0095-0.00080.33140.01840.03630.25950.01410.4554-10.5857-28.9877.5256
90.1781-0.1359-0.01560.3727-0.2170.18760.2280.37160.1953-0.273-0.2403-0.39330.07210.1449-0.00670.25410.0137-0.00180.68520.08990.716723.9423-5.597712.406
100.2573-0.2590.02090.36490.09220.3425-0.10180.04620.15520.6099-0.0193-0.2596-0.16330.05330.02610.394-0.0209-0.16790.5195-0.01590.553115.9395-0.282624.3691
110.4550.26780.1160.2697-0.16770.49070.0047-0.07060.05320.15130.00610.14220.2419-0.1544-00.48970.02540.01850.41470.00320.3018-18.0892-2.18725.7776
120.0876-0.0062-0.06030.0619-0.05070.0816-0.0621-0.15280.0002-0.15510.11710.2001-0.1118-0.4044-00.38890.04530.01960.45840.00980.4009-24.00482.275517.756
130.15110.02070.08940.0141-0.00090.0661-0.0515-0.1712-0.39990.08160.3116-0.01120.4109-0.79270.00160.6149-0.0830.04290.59390.0630.4489-30.001-10.196430.325
140.4745-0.10910.14470.1539-0.20410.2327-0.0510.10680.20780.0995-0.07490.0632-0.0854-0.0905-00.41810.0138-0.07120.3735-0.04380.3864-0.993511.208920.9963
150.01030.00050.00510.02840.01390.00750.00290.2623-0.33420.289-0.0163-0.0278-0.1740.34040.00010.56270.03850.00070.52360.01010.530414.0366-17.173521.6872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 143 )
2X-RAY DIFFRACTION2chain 'B' and (resid 144 through 418 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 234 )
4X-RAY DIFFRACTION4chain 'D' and (resid 235 through 295 )
5X-RAY DIFFRACTION5chain 'D' and (resid 296 through 418 )
6X-RAY DIFFRACTION6chain 'Y' and (resid 1 through 4 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 143 )
8X-RAY DIFFRACTION8chain 'A' and (resid 144 through 418 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 77 )
10X-RAY DIFFRACTION10chain 'C' and (resid 78 through 186 )
11X-RAY DIFFRACTION11chain 'C' and (resid 187 through 266 )
12X-RAY DIFFRACTION12chain 'C' and (resid 267 through 295 )
13X-RAY DIFFRACTION13chain 'C' and (resid 296 through 336 )
14X-RAY DIFFRACTION14chain 'C' and (resid 337 through 418 )
15X-RAY DIFFRACTION15chain 'X' and (resid 1 through 4 )

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