PDB-9j89: zbp1 nucleic acid complex

ID or keywords:

Entry

Database: PDB / ID: 9j89

Title

zbp1 nucleic acid complex

Components

DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')
RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')
Z-DNA-binding protein 1

Keywords

DNA BINDING PROTEIN/DNA/RNA / zbp1 / DNA BINDING PROTEIN-DNA-RNA complex

Function / homology

Function and homology information

ZBP1(DAI) mediated induction of type I IFNs / left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / IRF3 mediated activation of type 1 IFN / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / defense response to fungus ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 Å

Authors

Gao, A.M. / Zhou, C.

Funding support

China, 1items

Citation

Journal: Mol.Cell / Year: 2025
Title: ZBP1 senses spliceosome stress through Z-RNA:DNA hybrid recognition.
Authors: He, J. / Zhu, Y. / Tian, Z. / Liu, M. / Gao, A. / Fu, W. / Lu, F. / Sun, Y. / Guo, Y. / Pan, R. / Ji, Y. / Chen, J. / Lu, H. / Lin, J. / Liang, X. / Kim, C. / Zhou, C. / Jiao, H.

History

Deposition	Aug 20, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9j89.cif.gz	150.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9j89.ent.gz	113.7 KB	Display	PDB format
PDBx/mmJSON format	9j89.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/9j89 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/9j89	HTTPS FTP

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Related structure data

Related structure data	9j8gC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (3) #60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

C: DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')

G: DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')

D: Z-DNA-binding protein 1

F: Z-DNA-binding protein 1

H: Z-DNA-binding protein 1

A: Z-DNA-binding protein 1

E: RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')

B: RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')

hetero molecules

36.3 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')

D: Z-DNA-binding protein 1

A: Z-DNA-binding protein 1

B: RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')

hetero molecules

defined by author&software
Evidence: gel filtration
18.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')

F: Z-DNA-binding protein 1

H: Z-DNA-binding protein 1

E: RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')

hetero molecules

defined by author&software
18.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	30.240, 173.950, 30.440
Angle α, β, γ (deg.)	90.00, 94.42, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: DNA chain	DNA (5'-D(PCPAPCPGPCPA)-3') Mass: 1778.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein	Z-DNA-binding protein 1 / DNA-dependent activator of IFN-regulatory factors / DAI / Tumor stroma and activated macrophage protein DLM-1 Mass: 7154.361 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZBP1, C20orf183, DLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H171
#3: RNA chain	RNA (5'-R(PUPGPCPGPUPG)-3') Mass: 1908.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.54 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 1.58→21.57 Å / Num. obs: 42634 / % possible obs: 99.92 % / Redundancy: 6.2 % / CC_1/2: 0.995 / R_merge(I) obs: 0.1455 / Net I/σ(I): 9.34
Reflection shell	Resolution: 1.58→1.62 Å / Redundancy: 4.9 % / R_merge(I) obs: 1.546 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 2831 / CC_1/2: 0.32 / % possible all: 99.96

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4924: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.58→21.57 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2453	2066	4.85 %
R_work	0.2121	-	-
obs	0.2136	42619	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.58→21.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1988	500	11	291	2790

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.155
X-RAY DIFFRACTION	f_dihedral_angle_d	17.416	522
X-RAY DIFFRACTION	f_chiral_restr	0.063	420
X-RAY DIFFRACTION	f_plane_restr	0.009	370

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 (%)
1.58-1.62	0.4055	134	0.3621	2697	X-RAY DIFFRACTION	100
1.62-1.66	0.3572	148	0.3133	2684	X-RAY DIFFRACTION	100
1.66-1.7	0.3433	149	0.2905	2719	X-RAY DIFFRACTION	100
1.7-1.75	0.2973	126	0.2475	2661	X-RAY DIFFRACTION	100
1.75-1.81	0.284	144	0.2411	2700	X-RAY DIFFRACTION	100
1.81-1.87	0.2722	151	0.2325	2737	X-RAY DIFFRACTION	100
1.87-1.95	0.3068	147	0.2253	2653	X-RAY DIFFRACTION	100
1.95-2.04	0.2493	122	0.2118	2752	X-RAY DIFFRACTION	100
2.04-2.14	0.2282	150	0.2141	2677	X-RAY DIFFRACTION	100
2.14-2.28	0.2349	172	0.1995	2658	X-RAY DIFFRACTION	100
2.28-2.45	0.2253	124	0.199	2720	X-RAY DIFFRACTION	100
2.45-2.7	0.2469	135	0.2143	2707	X-RAY DIFFRACTION	100
2.7-3.09	0.2413	94	0.2093	2759	X-RAY DIFFRACTION	100
3.09-3.89	0.2243	154	0.1771	2702	X-RAY DIFFRACTION	100
3.89-21.57	0.2011	116	0.1968	2727	X-RAY DIFFRACTION	99

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	2.5444	-2.0426	-2.1164	5.3743	-0.9363	3.4475	0.0687	-0.3173	0.9089	0.3132	-0.3312	-0.3217	0.2753	0.2988	0.1431	0.0421	-0.0215	0.0014	0.1812	0.0079	0.3672	26.6862	-44.4405	12.4498
2	2.6807	-1.4693	2.1073	5.8089	-1.2002	1.6484	-0.1412	-0.168	-0.1548	0.4487	0.0863	0.3063	-0.4857	-0.0854	-0.0654	0.3107	-0.0044	0.0235	0.1566	-0.0283	0.0953	4.3129	-86.9114	-15.5508
3	3.382	-1.8001	2.9925	3.0003	-2.512	7.6928	-0.0016	-0.3611	0.0939	0.1366	-0.0883	0.0324	0.2515	-0.2591	0.0859	0.1065	-0.0334	0.029	0.1699	-0.0114	0.1507	14.8059	-59.2022	19.1205
4	3.5186	0.4988	0.886	4.2181	0.8782	3.4683	0.0823	-0.263	0.3381	0.1875	-0.0578	0.0662	0.0435	-0.0783	0.0197	0.0646	-0.0283	0.0425	0.1085	-0.0187	0.1309	18.0271	-53.3378	13.0782
5	4.747	1.0118	-0.3914	2.0106	-2.7603	3.5736	-0.0036	0.3408	0.0135	-1.1096	-0.0348	-0.0361	0.1974	0.1892	-0.2064	0.1084	-0.0087	0.0468	0.1381	-0.0025	0.16	16.7961	-54.6487	6.1813
6	8.3725	-0.3057	3.9579	2.8925	-1.0423	4.3978	-0.0577	0.0498	0.1102	0.0535	-0.1043	0.1913	0.1011	-0.1416	0.1936	0.1381	0.0049	0.0334	0.1372	-0.0404	0.1292	-2.8556	-67.2631	0.0277
7	5.6464	0.8512	1.8477	4.3255	1.4689	4.2604	0.0362	-0.4744	0.1221	0.5094	-0.2539	0.3963	0.2161	-0.5013	-0.0284	0.2665	-0.0461	0.0697	0.1864	-0.022	0.1585	1.3342	-76.0247	3.4752
8	5.8417	2.2817	-0.0595	7.8542	-0.4362	3.8519	-0.2011	0.4013	0.0586	-0.1077	0.1114	0.495	0.3575	-0.3254	0.1175	0.1828	-0.0128	0.03	0.155	-0.0348	0.0948	1.9467	-72.8294	-8.0761
9	3.8979	-1.1308	-0.5523	5.5059	-2.1529	4.3181	-0.0189	0.2124	0.133	0.1666	-0.1114	-0.3604	0.0263	0.3341	0.1648	0.1045	-0.0058	0.0102	0.1289	-0.0137	0.1152	10.0082	-70.0143	-3.0301
10	8.7036	-0.5409	-2.8874	1.7843	-0.5481	3.3795	0.0435	-0.0769	0.0656	-0.1782	0.0412	0.1826	-0.1574	-0.0621	-0.0083	0.2406	-0.0179	-0.0518	0.1258	-0.0213	0.2148	-2.1352	-101.7683	-26.9516
11	7.6508	-0.0173	-1.5776	2.7943	0.6241	3.7536	-0.3158	0.6783	0.1895	-0.51	0.1386	0.2632	-0.3394	-0.1566	0.0389	0.3533	-0.034	-0.0642	0.1813	0.0215	0.1831	2.4965	-93.0118	-30.6742
12	4.2133	-1.2047	0.8567	6.4878	-1.1269	4.168	-0.0244	-0.3982	-0.1409	0.5099	0.1478	0.2937	-0.1244	0.0162	-0.2468	0.1867	0.0047	-0.0327	0.1373	-0.0141	0.0844	5.0249	-97.9375	-19.9209
13	5.2714	0.4126	0.3277	9.5167	1.9547	6.947	-0.1769	0.1996	-0.1742	-0.2724	0.336	-0.7024	-0.1826	0.434	0.0204	0.1712	-0.0353	0.0031	0.1629	-0.0344	0.1789	10.4875	-96.6648	-25.8324
14	5.2396	-2.1234	-3.5881	2.6858	2.4158	7.8147	-0.3092	-0.2553	-0.2883	-0.0328	0.0154	0.1292	-0.1412	0.4548	0.1976	0.205	-0.0414	-0.0319	0.1896	0.0053	0.3687	42.6844	-23.5034	16.0169
15	3.9291	0.7931	0.156	3.6839	-0.4128	3.8285	-0.0014	-0.322	0.1254	0.1718	-0.0353	-0.1935	-0.1205	0.2417	0.0373	0.1276	-0.0294	-0.0079	0.1411	-0.002	0.2621	39.9336	-31.1394	12.9436
16	4.2731	-2.0785	-0.5985	7.8404	1.4277	3.0968	0.2604	0.6292	0.5838	-1.1411	-0.1025	-0.0946	-0.5083	-0.0147	-0.0609	0.1822	0.0043	-0.0074	0.1438	0.0293	0.2462	38.2505	-28.2553	4.1927
17	4.9669	0.3572	-3.8996	3.6372	-1.079	3.2897	0.2208	0.5128	-0.0161	0.0413	-0.2726	0.195	0.6087	-0.3602	-0.1348	0.4793	0.0028	0.0081	0.1756	-0.0168	0.135	4.2994	-81.6886	-11.6931
18	2.7418	0.0584	2.5225	4.4339	-0.8857	3.0635	0.1663	-0.2472	-0.2163	0.1631	-0.2268	0.5096	-0.083	-0.2403	0.0334	0.093	-0.0058	0.0193	0.1722	-0.0348	0.3624	30.5343	-38.8607	12.0561

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 201 through 206 )
2	X-RAY DIFFRACTION	2	chain 'G' and (resid 201 through 206 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 7 through 25 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 26 through 62 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 63 through 70 )
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 7 through 25 )
7	X-RAY DIFFRACTION	7	chain 'F' and (resid 26 through 41 )
8	X-RAY DIFFRACTION	8	chain 'F' and (resid 42 through 54 )
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 55 through 70 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 7 through 25 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 26 through 41 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 42 through 62 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 63 through 69 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 7 through 25 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 26 through 54 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 55 through 69 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 1 through 6 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 1 through 6 )

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