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

ID or keywords:

Entry

Database: PDB / ID: 9jxx

Title

Crystal structure of SiRe_0806 in complex with cA4

Components

PIN domain-containing protein
RNA (5'-R(P*AP*AP*AP*A)-3')

Keywords

IMMUNE SYSTEM/RNA / Sulfolobus islandicus / SiRe_0806 / cyclic oligo-adenylates (cOAs) / CARF domain / PIN domain / RNase / IMMUNE SYSTEM-RNA complex

Function / homology

RNA / PIN domain-containing protein

Function and homology information

Biological species

Saccharolobus islandicus REY15A (archaea)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Wang, F. / Zhao, P. / Bi, X. / She, Q.

Funding support

China, 1items

Citation

Journal: 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

Deposition	Oct 12, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jul 23, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 3, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9jxx.cif.gz	680.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9jxx.ent.gz	562.5 KB	Display	PDB format
PDBx/mmJSON format	9jxx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9jxx_validation.pdf.gz	490.7 KB	Display	wwPDB validaton report
Full document	9jxx_full_validation.pdf.gz	510.7 KB	Display
Data in XML	9jxx_validation.xml.gz	63.8 KB	Display
Data in CIF	9jxx_validation.cif.gz	83.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jx/9jxx ftp://data.pdbj.org/pub/pdb/validation_reports/jx/9jxx	HTTPS FTP

-
Related structure data

Related structure data	9jxwC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

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')

201 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

2

B: PIN domain-containing protein

D: PIN domain-containing protein

Y: RNA (5'-R(P*AP*AP*AP*A)-3')

defined by author&software
100 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: PIN domain-containing protein

C: PIN domain-containing protein

X: RNA (5'-R(P*AP*AP*AP*A)-3')

defined by author&software
100 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1

#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(PAPAPAPA)-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 modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.9 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH=8.0; 40% MPD

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→48.82 Å / Num. obs: 58836 / % possible obs: 92.7 % / Redundancy: 3.6 % / R_merge(I) obs: 0.038 / Net I/σ(I): 11.3
Reflection shell	Resolution: 2.5→2.57 Å / R_merge(I) obs: 0.361 / Num. unique obs: 4703

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2444	2897	4.93 %
R_work	0.2062	-	-
obs	0.2082	58808	92.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→48.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13410	176	0	76	13662

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13823
X-RAY DIFFRACTION	f_angle_d	0.542	18675
X-RAY DIFFRACTION	f_dihedral_angle_d	7.696	1932
X-RAY DIFFRACTION	f_chiral_restr	0.042	2123
X-RAY DIFFRACTION	f_plane_restr	0.004	2356

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.54	0.3252	138	0.3147	2746	X-RAY DIFFRACTION	94
2.54-2.58	0.3638	151	0.2956	2654	X-RAY DIFFRACTION	94
2.58-2.63	0.3183	115	0.2875	2730	X-RAY DIFFRACTION	94
2.63-2.68	0.276	141	0.2774	2620	X-RAY DIFFRACTION	92
2.68-2.74	0.3085	117	0.2608	2614	X-RAY DIFFRACTION	89
2.74-2.8	0.3375	117	0.2449	2346	X-RAY DIFFRACTION	82
2.8-2.86	0.2933	133	0.2437	2795	X-RAY DIFFRACTION	96
2.86-2.93	0.2722	138	0.2484	2804	X-RAY DIFFRACTION	96
2.93-3.01	0.302	155	0.2589	2707	X-RAY DIFFRACTION	96
3.01-3.1	0.3387	163	0.2663	2719	X-RAY DIFFRACTION	96
3.1-3.2	0.3095	148	0.2516	2728	X-RAY DIFFRACTION	95
3.2-3.32	0.2724	145	0.2235	2712	X-RAY DIFFRACTION	94
3.32-3.45	0.3009	146	0.222	2649	X-RAY DIFFRACTION	93
3.45-3.61	0.2765	127	0.2239	2445	X-RAY DIFFRACTION	86
3.61-3.8	0.2361	114	0.2173	2701	X-RAY DIFFRACTION	92
3.8-4.03	0.2391	151	0.1906	2743	X-RAY DIFFRACTION	96
4.03-4.34	0.2408	118	0.1755	2771	X-RAY DIFFRACTION	95
4.34-4.78	0.232	115	0.1654	2708	X-RAY DIFFRACTION	93
4.78-5.47	0.1852	129	0.1765	2489	X-RAY DIFFRACTION	87
5.47-6.89	0.243	185	0.2044	2694	X-RAY DIFFRACTION	96
6.89-48.82	0.1553	151	0.1545	2536	X-RAY DIFFRACTION	89

Refinement TLS params.

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

ID	L11 (°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)
1	0.2669	-0.1821	-0.1752	0.6203	0.1601	0.1182	-0.0569	0.136	0.0681	-0.4175	-0.0861	-0.203	-0.2903	0.2405	-0.0254	0.6143	-0.2037	0.1525	0.6847	0.0405	0.3836	16.703	29.334	-27.7655
2	0.6253	0.6003	-0.3809	0.5731	-0.7139	1.0404	-0.0834	0.101	0.1702	0.0528	0.1056	0.2526	-0.1532	-0.0165	-0.0061	0.3481	-0.0534	-0.0469	0.275	-0.004	0.3763	-10.9932	28.6424	-7.1083
3	0.4546	0.3443	-0.2655	0.7574	-0.232	0.2239	0.0766	-0.0969	-0.2757	-0.666	-0.0961	-0.3069	0.1126	0.1537	0.2094	0.2143	0.0699	0.2799	0.4701	-0.01	0.3714	11.6518	2.3365	-21.7425
4	0.4695	-0.3235	0.1045	0.2354	-0.0836	0.0654	0.0555	0.022	-0.2179	-0.2293	0.035	0.1188	-0.3057	-0.1519	0.0108	0.4589	-0.0506	-0.0224	0.3387	-0.0256	0.3046	-23.5023	-0.8912	-18.3178
5	0.7386	0.1796	-0.0813	0.2503	-0.2519	0.2823	-0.1298	-0.029	-0.1844	-0.1875	-0.0026	-0.0596	-0.1838	0.0098	-0.0002	0.4942	0.0631	0.0315	0.4073	-0.0122	0.3557	-10.2505	-5.2079	-23.7363
6	0.0244	0.0227	0.0229	0.0213	0.0192	0.0148	-0.2291	0.0019	0.2793	-0.3048	-0.1007	0.0058	0.225	0.3586	0.0001	0.653	-0.0723	0.0357	0.6634	0.0283	0.4922	13.6319	17.0119	-21.5145
7	0.3848	0.2613	-0.0472	0.6458	0.1381	0.2953	-0.1677	-0.0907	-0.1048	0.4362	0.0216	-0.2636	0.1747	0.062	-0.0041	0.5302	0.1679	-0.1341	0.5076	0.0276	0.4292	17.8603	-29.428	27.775
8	0.8106	-0.9262	0.4852	0.6269	-0.5848	0.9293	-0.0433	-0.0834	-0.2355	-0.1124	0.1097	0.2668	0.1413	0.0095	-0.0008	0.3314	0.0184	0.0363	0.2595	0.0141	0.4554	-10.5857	-28.987	7.5256
9	0.1781	-0.1359	-0.0156	0.3727	-0.217	0.1876	0.228	0.3716	0.1953	-0.273	-0.2403	-0.3933	0.0721	0.1449	-0.0067	0.2541	0.0137	-0.0018	0.6852	0.0899	0.7167	23.9423	-5.5977	12.406
10	0.2573	-0.259	0.0209	0.3649	0.0922	0.3425	-0.1018	0.0462	0.1552	0.6099	-0.0193	-0.2596	-0.1633	0.0533	0.0261	0.394	-0.0209	-0.1679	0.5195	-0.0159	0.5531	15.9395	-0.2826	24.3691
11	0.455	0.2678	0.116	0.2697	-0.1677	0.4907	0.0047	-0.0706	0.0532	0.1513	0.0061	0.1422	0.2419	-0.1544	-0	0.4897	0.0254	0.0185	0.4147	0.0032	0.3018	-18.0892	-2.187	25.7776
12	0.0876	-0.0062	-0.0603	0.0619	-0.0507	0.0816	-0.0621	-0.1528	0.0002	-0.1551	0.1171	0.2001	-0.1118	-0.4044	-0	0.3889	0.0453	0.0196	0.4584	0.0098	0.4009	-24.0048	2.2755	17.756
13	0.1511	0.0207	0.0894	0.0141	-0.0009	0.0661	-0.0515	-0.1712	-0.3999	0.0816	0.3116	-0.0112	0.4109	-0.7927	0.0016	0.6149	-0.083	0.0429	0.5939	0.063	0.4489	-30.001	-10.1964	30.325
14	0.4745	-0.1091	0.1447	0.1539	-0.2041	0.2327	-0.051	0.1068	0.2078	0.0995	-0.0749	0.0632	-0.0854	-0.0905	-0	0.4181	0.0138	-0.0712	0.3735	-0.0438	0.3864	-0.9935	11.2089	20.9963
15	0.0103	0.0005	0.0051	0.0284	0.0139	0.0075	0.0029	0.2623	-0.3342	0.289	-0.0163	-0.0278	-0.174	0.3404	0.0001	0.5627	0.0385	0.0007	0.5236	0.0101	0.5304	14.0366	-17.1735	21.6872

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 143 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 144 through 418 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 1 through 234 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 235 through 295 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 296 through 418 )
6	X-RAY DIFFRACTION	6	chain 'Y' and (resid 1 through 4 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1 through 143 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 144 through 418 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 77 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 78 through 186 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 187 through 266 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 267 through 295 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 296 through 336 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 337 through 418 )
15	X-RAY DIFFRACTION	15	chain 'X' and (resid 1 through 4 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi