PDB-8zbf: Crystal structure of the A58-T10 DNA aptamer in complex with SARS...

ID or keywords:

Entry

Database: PDB / ID: 8zbf

Title

Crystal structure of the A58-T10 DNA aptamer in complex with SARS-CoV-2 N-NTD

Components

DNA (40-MER)
Nucleoprotein

Keywords

DNA / aptamer / A58 / nucleocapsid protein / SARS-CoV-2

Function / homology

Function and homology information

response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Chen, X. / Huang, L.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Molecular characterization and broad-spectrum mechanism of coronavirus N protein aptamer
Authors: Chen, X. / Huang, L.

History

Deposition	Apr 26, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2025	Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zbf.cif.gz	374.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8zbf.ent.gz	301.8 KB	Display	PDB format
PDBx/mmJSON format	8zbf.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/zb/8zbf ftp://data.pdbj.org/pub/pdb/validation_reports/zb/8zbf	HTTPS FTP

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Related structure data

Related structure data	6m3mS S: Starting model for refinement
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	#255 - Mar 2021 Cisplatin and DNA similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #23 - Nov 2001 DNA similarity (2) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #245 - May 2020 Spliceosomes similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

E: DNA (40-MER)

F: DNA (40-MER)

G: DNA (40-MER)

H: DNA (40-MER)

hetero molecules

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

1

A: Nucleoprotein

B: Nucleoprotein

E: DNA (40-MER)

F: DNA (40-MER)

hetero molecules

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

2

C: Nucleoprotein

D: Nucleoprotein

G: DNA (40-MER)

H: DNA (40-MER)

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.970, 92.480, 77.920
Angle α, β, γ (deg.)	90.00, 90.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Nucleoprotein / N / Nucleocapsid protein / NC / Protein N Mass: 14837.537 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: DNA chain	DNA (40-MER) Mass: 12345.954 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
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: 2.35 Å³/Da / Density % sol: 47.69 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978565 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978565 Å / Relative weight: 1
Reflection	Resolution: 2.8→35.48 Å / Num. obs: 24893 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.167 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 6.8 % / R_merge(I) obs: 1.322 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1854 / CC_1/2: 0.681

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
xia2		data reduction
xia2		data scaling
PHENIX	(1.20.1_4487)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB 6M3M and Double stranded DNA built by coot nucleotide builder

6m3m

Resolution: 2.8→35.48 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 31.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2609	1138	4.59 %
R_work	0.2166	-	-
obs	0.2187	24816	99.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→35.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3801	3235	2	0	7038

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7540
X-RAY DIFFRACTION	f_angle_d	0.914	10919
X-RAY DIFFRACTION	f_dihedral_angle_d	27.739	3156
X-RAY DIFFRACTION	f_chiral_restr	0.053	1179
X-RAY DIFFRACTION	f_plane_restr	0.015	862

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 (%)
2.8-2.93	0.4045	156	0.3488	2941	X-RAY DIFFRACTION	100
2.93-3.08	0.2994	145	0.3316	2954	X-RAY DIFFRACTION	100
3.08-3.27	0.3986	119	0.3068	2912	X-RAY DIFFRACTION	98
3.27-3.53	0.3141	138	0.25	2960	X-RAY DIFFRACTION	99
3.53-3.88	0.2689	142	0.2213	2964	X-RAY DIFFRACTION	100
3.88-4.44	0.2263	154	0.1905	2943	X-RAY DIFFRACTION	100
4.44-5.59	0.2289	139	0.1836	2994	X-RAY DIFFRACTION	100
5.59-35.48	0.2143	145	0.1723	3010	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	3.3033	1.3766	-1.9186	2.8853	-1.3821	2.6354	0.0439	-0.2235	-0.1095	0.3151	-0.0188	-0.0721	0.0875	0.3608	0.0735	0.4152	0.022	0.0048	0.3338	-0.0193	0.4322	75.1606	6.7642	-41.445
2	6.8511	1.6926	-0.0663	5.1565	-0.2782	2.8384	-0.0285	0.8017	1.4309	-0.218	0.1411	0.0664	-0.741	0.3174	-0.1431	0.43	-0.0301	0.0857	0.3533	0.0213	0.5308	75.2892	18.1266	-47.5031
3	1.0807	1.5887	0.2536	3.3703	-0.589	1.2904	-0.4471	0.341	-0.55	-0.1513	0.0762	-0.163	0.2945	0.1184	0.1737	0.4533	0.0103	0.0825	0.4798	0.0201	0.463	72.0784	3.0733	-49.7895
4	0.6156	0.6022	-1.5643	0.9551	-1.6506	3.9378	0.583	-0.9892	0.035	-0.588	-1.1572	-1.3005	-0.6704	0.0192	0.2681	0.608	0.0781	0.0448	0.5571	-0.0019	0.5327	4.2974	8.8433	2.9295
5	3.7756	-0.2782	-0.7646	5.4423	2.3551	6.4468	0.0118	0.15	-0.1009	-0.4268	-0.2777	0.4465	-0.4281	-1.2396	0.1538	0.3521	0.0836	0.0356	0.7487	-0.0164	0.43	-6.4341	6.3206	2.6716
6	2.2099	1.246	3.514	8.7164	0.1502	6.1931	-0.2698	-0.5413	1.6911	-1.6515	-0.9201	1.5146	-2.3913	-1.7509	-0.3221	1.2198	0.1673	0.0276	-0.2228	0.4227	0.2777	-1.0121	19.244	4.9548
7	6.3614	1.499	2.0196	7.6566	5.2472	7.0898	0.1616	-0.7001	-0.622	0.4053	-0.235	-0.3054	0.5996	-0.3915	-0.2127	0.386	0.061	0.0112	0.6062	0.1382	0.4215	-0.6398	1.8038	9.637
8	4.3426	-0.686	3.3012	0.293	-0.4858	2.5313	0.5904	-0.3752	-2.7295	0.0953	0.1923	-0.1846	-0.5318	0.028	-0.5519	0.4316	0.0175	0.004	0.5255	0.0607	0.6136	-29.4707	17.6793	-47.6145
9	2.6134	-0.507	2.5625	1.1223	-0.882	3.3015	0.2671	-0.2183	-0.1668	-0.1855	0.0435	0.6924	-0.4951	-1.0264	-0.0439	0.5134	0.0935	0.0556	0.6282	0.0619	0.7343	-45.4801	24.2566	-50.7417
10	6.166	0.4677	3.016	3.419	-1.3043	2.9827	0.4187	-0.5842	-0.4888	0.3165	-0.0211	0.3511	0.1403	-0.4637	-0.3705	0.4395	0.0247	0.0513	0.4185	0.0656	0.6248	-36.8454	19.7904	-45.9361
11	8.8448	-1.734	-3.2402	6.0725	1.0821	5.9647	0.4165	0.0126	-0.6039	-0.0147	-0.1415	0.0632	1.2156	-1.7013	-0.4502	0.4162	-0.0144	-0.1029	0.4837	0.1245	0.8038	-45.3799	11.5659	-47.9821
12	5.3757	1.7935	3.1496	5.8024	0.51	3.2917	0.782	-0.7508	-2.0822	0.4073	-0.0898	0.0364	1.4158	-0.165	-0.6726	0.6158	0.1168	-0.069	0.5169	0.0981	0.8882	-33.3744	7.0584	-50.4291
13	3.3313	0.7274	2.1792	3.7662	0.5345	5.4301	-0.2713	0.8099	0.4152	0.0633	-0.1329	0.1216	-0.4868	0.0602	0.3641	0.3968	0.0109	-0.0135	0.3233	0.0504	0.4267	-35.6121	24.4892	-54.2275
14	1.7322	0.1445	1.2955	0.9274	0.2298	4.0245	0.0576	-0.2297	-0.1765	-0.4074	-0.1161	-0.3287	0.4195	1.3457	-0.1195	0.5306	0.1466	-0.0376	0.7926	-0.2503	0.5629	40.1998	23.4823	2.9449
15	1.4245	1.1659	-0.0068	8.3139	-1.613	6.8935	0.2517	0.494	-0.3998	-0.4959	-0.081	-0.2413	0.5546	1.0818	-0.1015	0.3934	0.2964	0.0182	1.024	-0.107	0.7233	40.9872	16.0399	1.4955
16	5.1209	4.693	0.6859	8.5666	0.1362	0.1587	0.1956	1.3436	0.8733	-1.7687	-0.264	1.4385	-0.2853	1.9339	0.1017	0.8706	-0.2861	-0.0169	1.4051	-0.1311	0.4697	34.5065	35.9191	-13.1175
17	4.8394	-0.4951	1.4698	4.5096	-0.7541	5.0793	0.0627	0.5338	-0.8019	-0.3715	-0.1442	0.2833	0.7537	0.7076	0.0517	0.606	0.1665	-0.0233	0.8561	-0.251	0.6148	38.8692	15.3399	-1.2575
18	1.4755	-1.9098	-0.2025	2.8913	0.1558	0.9391	0.1088	-0.9461	0.6036	1.1914	0.4367	-0.0535	-1.5912	1.2568	0.0136	0.6812	-0.0923	-0.0622	1.0422	0.0237	0.4846	42.4635	29.96	8.4303
19	8.9729	2.8059	-3.6773	4.2828	-2.957	4.2337	-0.2394	-0.8883	0.5974	0.2831	0.1305	1.1206	0.3509	-1.014	0.0056	0.5411	0.0731	0.0628	0.7427	-0.0143	0.7779	56.0769	-0.3891	-31.7689
20	9.8745	0.8779	-2.7298	0.9169	-1.2577	2.5006	-0.5425	-0.3078	-0.3838	-0.2218	0.1161	-0.4774	-0.0455	0.9026	0.4059	0.7395	-0.013	0.0191	1.3598	-0.1749	0.9555	25.0822	-0.5221	-19.9393
21	7.162	-1.9778	-0.69	3.6786	-0.465	4.6577	0.1528	0.1712	-0.0234	-0.1723	-0.1908	0.1578	0.3159	0.5052	0.0944	0.4326	-0.0091	0.0673	0.4828	-0.0675	0.6297	13.8647	-0.8353	-7.5717
22	7.258	-3.4674	-2.5857	2.2628	-0.1274	3.9473	-0.4106	0.8635	-0.6254	-0.5642	-0.7396	-0.3446	-1.7205	0.6429	1.2065	0.643	-0.0625	0.0009	0.9309	-0.0466	0.8856	23.1259	0.1111	-12.281
23	9.0543	-0.3785	-1.7072	1.2062	-0.4067	1.9532	-0.5891	-0.2112	-0.0888	0.3073	-0.0781	0.1109	-0.0358	-0.1544	0.4418	0.668	0.1044	0.0895	1.5138	-0.1507	0.8254	48.5895	-0.1151	-20.0849
24	8.1598	-1.8566	-1.343	2.2023	1.5425	2.0291	0.6858	-0.846	-1.0176	0.8543	-0.0522	-1.1166	1.6021	-2.4647	-0.6495	0.8625	-0.144	-0.0053	1.7738	0.1895	1.1611	-27.6137	21.696	-21.917
25	8.9725	-0.4404	2.079	3.3094	1.4154	4.1738	-0.3357	-1.6044	0.5383	0.6236	0.0975	1.5559	-0.4713	-0.2679	0.727	0.7743	0.0994	0.0882	0.8229	-0.0956	0.9476	-22.1845	33.7662	-35.0722
26	5.8103	1.2927	0.9506	3.1934	-1.0277	1.7516	-0.2518	0.4433	0.4429	-0.2742	0.2191	-0.7529	-0.2617	0.0903	0.0214	0.5496	0.0332	0.0886	0.463	-0.0513	0.7011	-19.9542	29.4206	-43.3515
27	5.3111	0.9437	1.1699	2.9831	-1.5155	1.5642	-0.3858	-0.7463	-0.5841	-0.089	-0.0944	-0.2661	0.9449	1.2544	0.0457	0.7304	0.0748	0.1109	0.9062	0.0389	0.8596	-10.8991	25.0262	-34.2333
28	2.6936	-0.5815	2.9941	1.5875	1.1786	4.2189	-0.9609	-0.097	-0.2016	0.4111	0.278	0.1409	0.0008	-0.2422	0.6552	0.7093	-0.0768	0.0476	1.0674	-0.0503	0.7639	10.5151	28.3878	-23.6398
29	6.8484	-2.2534	3.6498	5.4566	1.9963	7.2391	-0.2811	0.0336	0.0028	-0.2752	0.4204	0.0531	-0.0847	0.0793	-0.1295	0.3817	-0.0488	0.0238	0.7137	-0.0734	0.6977	21.5803	28.8259	-11.5445
30	9.3162	2.1095	2.5627	-0.2143	0.214	0.0138	-0.5321	-0.2072	-0.4554	0.0794	0.1597	0.3515	-0.0113	-0.5006	0.4417	0.6465	-0.0164	0.0902	1.2164	-0.0501	1.1107	-6.0266	27.7694	-21.6569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 48 through 129 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 130 through 149 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 150 through 173 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 48 through 55 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 56 through 139 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 140 through 149 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 150 through 173 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 48 through 55 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 56 through 73 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 74 through 118 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 119 through 139 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 140 through 149 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 150 through 173 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 49 through 78 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 79 through 90 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 91 through 106 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 107 through 159 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 160 through 173 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 25 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 26 through 40 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 1 through 20 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 22 through 26 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 27 through 40 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 1 through 5 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 6 through 10 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 11 through 20 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 21 through 25 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 26 through 40 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 1 through 20 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 22 through 40 )

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