PDB-4lnq: Crystal structure of Ifi202 HINa domain in complex with 20bp dsDNA

ID or keywords:

Entry

Database: PDB / ID: 4lnq

Title

Crystal structure of Ifi202 HINa domain in complex with 20bp dsDNA

Components

20bp DNA
Interferon-activable protein 202

Keywords

DNA BINDING PROTEIN/DNA / OB fold /

DNA binding / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / negative regulation of innate immune response / activation of innate immune response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization /

double-stranded DNA binding / protein homotetramerization / molecular adaptor activity /

inflammatory response ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Li, H. / Wang, Z.-X. / Wu, J.-W.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structural mechanism of DNA recognition by the p202 HINa domain: insights into the inhibition of Aim2-mediated inflammatory signalling.
Authors: Li, H. / Wang, J. / Wang, J. / Cao, L.S. / Wang, Z.X. / Wu, J.W.

History

Deposition	Jul 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4lnq.cif.gz	223.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4lnq.ent.gz	176.5 KB	Display	PDB format
PDBx/mmJSON format	4lnq.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/ln/4lnq ftp://data.pdbj.org/pub/pdb/validation_reports/ln/4lnq	HTTPS FTP

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Related structure data

Related structure data	3b6yS S: Starting model for refinement
Similar structure data	4auq-d 7ai0-d 7ai1-d 5aiu-d 6sqo-d 4ap4-d 5vzw-d 6s53-1 5xbj-d 5d6b-d Search similar-shape structures by Omokage search (details) 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Interferon-activable protein 202

B: Interferon-activable protein 202

C: 20bp DNA

D: 20bp DNA

57.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	95.353, 105.566, 65.143
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Interferon-activable protein 202 / Ifi-202 / Interferon-inducible protein p202 / Lupus susceptibility protein p202 Mass: 22599.061 Da / Num. of mol.: 2 / Fragment: UNP residues 53-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifi202, Ifi202a, Ifi202b / Plasmid: pETduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q9R002
#2: DNA chain	20bp DNA Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: dsDNA(5'-CCATCAAAGATCTTTGATGG-3')
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.95 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris, pH 5.5, 0.2M ammonium acetate, 10mM strontium chloride and 17% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2012
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2→40 Å / Num. obs: 44832 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / R_merge(I) obs: 0.096 / Net I/σ(I): 27.4
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 7.9 % / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B6Y

3b6y

Resolution: 2→36.148 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2343	2253	5.04 %
R_work	0.1999	-	-
obs	0.2016	44746	99.38 %
all	-	31663	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.39 Å² / k_sol: 0.35 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.3539 Å²	0 Å²	0 Å²
2-	-	11.8543 Å²	-0 Å²
3-	-	-	-4.5004 Å²

Refinement step

Cycle: LAST / Resolution: 2→36.148 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3123	814	0	327	4264

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4097
X-RAY DIFFRACTION	f_angle_d	1.116	5675
X-RAY DIFFRACTION	f_dihedral_angle_d	22.079	1605
X-RAY DIFFRACTION	f_chiral_restr	0.077	627
X-RAY DIFFRACTION	f_plane_restr	0.004	579

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 (%)
2-2.0457	0.3187	136	0.2577	2502	X-RAY DIFFRACTION	95
2.0457-2.0933	0.2635	149	0.2451	2634	X-RAY DIFFRACTION	100
2.0933-2.1457	0.3074	138	0.2254	2626	X-RAY DIFFRACTION	100
2.1457-2.2037	0.278	136	0.2203	2616	X-RAY DIFFRACTION	100
2.2037-2.2685	0.2906	128	0.2157	2659	X-RAY DIFFRACTION	100
2.2685-2.3417	0.2983	126	0.2191	2648	X-RAY DIFFRACTION	100
2.3417-2.4254	0.305	147	0.2237	2627	X-RAY DIFFRACTION	100
2.4254-2.5225	0.2342	140	0.2088	2660	X-RAY DIFFRACTION	100
2.5225-2.6372	0.2698	152	0.2077	2632	X-RAY DIFFRACTION	100
2.6372-2.7762	0.2733	137	0.2118	2633	X-RAY DIFFRACTION	100
2.7762-2.9501	0.261	145	0.2195	2692	X-RAY DIFFRACTION	100
2.9501-3.1778	0.2442	151	0.2206	2658	X-RAY DIFFRACTION	100
3.1778-3.4973	0.244	144	0.2037	2652	X-RAY DIFFRACTION	99
3.4973-4.0028	0.2217	150	0.1913	2702	X-RAY DIFFRACTION	100
4.0028-5.0409	0.1693	146	0.1541	2738	X-RAY DIFFRACTION	100
5.0409-36.1534	0.1891	128	0.1897	2814	X-RAY DIFFRACTION	98

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	1.6332	2.7001	-2.0785	8.2781	-3.7193	7.5469	-0.0421	0.2951	-0.8277	0.1538	0.1859	0.3139	0.3936	-1.3807	-0.1004	0.2452	-0.0861	-0.0421	0.3735	0.0204	0.3784	24.5603	119.1686	-18.6104
2	3.7458	2.1629	-1.4737	5.4419	-1.8983	5.1533	-0.3323	0.0538	-0.5287	-0.0501	0.0216	-0.0138	0.5371	-0.2568	0.1871	0.248	-0.0267	0.0805	0.1318	-0.0692	0.346	29.5535	110.6375	-6.2881
3	4.0974	0.7559	-0.1899	5.2206	-0.5798	3.9295	-0.1455	0.1593	-0.5167	-0.1074	0.017	-0.2447	0.1322	0.2988	0.0928	0.1694	-0.0335	0.0704	0.1173	-0.0349	0.2704	35.0472	115.7809	-11.5178
4	3.7879	-0.5762	-2.1944	4.9386	1.4451	6.1951	-0.0809	0.4626	-0.7004	-0.375	0.1306	0.0314	0.5597	-0.1067	-0.0215	0.2585	-0.0586	0.0324	0.1282	-0.0829	0.3651	30.5407	114.2366	-16.1139
5	3.7729	-3.6293	-4.4455	5.5719	4.9214	7.4966	-0.4077	0.4801	-0.6463	-0.4971	0.4726	-0.784	0.1203	0.8371	-0.182	0.2509	-0.1809	0.2439	0.4723	-0.1487	0.6147	47.9671	120.4155	-16.3576
6	7.4628	-0.8634	-5.7925	0.9848	0.4728	5.5887	0.2169	-0.6624	0.7928	0.08	0.0406	-0.3771	-0.6562	0.6725	-0.2588	0.3476	-0.1283	0.0035	0.1571	-0.0458	0.2952	34.7933	130.2779	2.108
7	5.4676	1.7681	-0.8167	3.4561	0.2294	4.3613	0.2263	-0.6286	-0.1603	0.5331	-0.0494	0.0757	-0.2297	0.1124	-0.1605	0.2209	0.0249	0.0499	0.1747	0.0196	0.2048	22.3362	120.9199	10.0923
8	4.9941	1.7818	1.4428	2.1295	2.8366	4.9387	0.1546	-0.5984	-0.5487	0.3928	0.0147	-0.3755	0.2965	0.2183	-0.1132	0.1883	0.0015	0.0029	0.1852	0.0775	0.1792	24.4323	116.7917	11.3442
9	7.1402	0.1991	1.0145	6.3512	0.4401	6.8151	-0.0347	-0.2564	-0.0006	0.1567	0.107	0.2365	-0.3062	-0.1572	-0.0906	0.1619	-0.0231	0.0592	0.1171	0.0345	0.1508	22.5028	120.9762	4.4305
10	7.0257	0.5753	-0.015	4.759	1.8657	6.7451	-0.1175	-1.158	0.1384	0.628	0.2107	0.2214	-0.0887	-0.6778	0.001	0.2831	0.1271	0.0713	0.3853	0.0661	0.2957	-24.2477	120.8783	44.7245
11	1.8425	-2.8998	0.5585	6.4275	0.0737	7.0811	0.0161	-0.2088	-0.9028	0.0219	0.0754	-0.4801	1.1115	0.5608	-0.2665	0.354	0.0953	0.0528	0.2004	0.1125	0.5346	-13.8101	107.5024	33.1024
12	6.5671	-2.0689	-1.779	3.2774	0.5632	4.7503	0.0231	-0.4836	-0.5734	0.1146	0.2116	0.3875	0.048	-0.7008	-0.125	0.1974	0.0367	0.0694	0.3469	0.1183	0.2806	-26.2163	116.2922	38.9375
13	5.1499	0.2388	-1.4164	2.2573	-0.516	2.3924	0.0007	-1.1164	-0.4078	0.5403	0.2688	0.3524	-0.1525	-0.351	-0.0704	0.2598	0.0896	0.0688	0.517	0.071	0.2536	-25.8967	118.6592	45.107
14	3.1577	0.0593	-1.6018	1.7911	-0.5698	3.7389	-0.1315	-0.0743	0.3043	0.3222	0.2297	0.4206	-0.3311	-0.5425	-0.2667	0.2406	0.115	0.0551	0.1924	-0.0153	0.2697	-25.3202	130.3281	25.8082
15	4.3242	-2.4474	-0.4001	3.7319	0.0587	2.2919	0.186	0.5251	-0.2417	-0.616	-0.062	-0.1217	-0.1189	0.0003	-0.0933	0.2253	-0.0163	0.0311	0.1318	-0.0833	0.2496	-13.2864	122.5219	17.3761
16	6.7332	-1.5167	1.5519	5.6513	2.6952	2.1026	0.5449	0.8631	-1.629	-0.4137	0.1812	-0.4778	0.5161	0.667	-0.7019	0.4473	-0.0065	0.0143	0.3298	-0.1806	0.7382	-14.0772	111.445	16.0317
17	6.0844	-0.2633	0.9231	4.8381	-0.48	6.1927	-0.0367	0.0318	0.0215	-0.4504	0.0369	-0.0437	-0.0717	0.0907	0.0443	0.1393	0.0279	0.066	0.0006	-0.0585	0.1785	-13.7839	120.4923	22.6957
18	0.2969	-0.0038	-0.1589	0.1517	-0.0569	1.1295	0.2802	-0.1385	0.2028	-0.0296	0.0863	0.0199	0.0608	-0.1375	0.5852	0.1627	0.0522	0.0659	0.4958	-0.1836	-0.0452	4.9485	122.5848	14.3971
19	0.2391	-0.0175	0.0137	0.1781	0.0932	0.0475	0.1025	0.1319	0.2163	-0.0343	0.1484	0.0309	0.0589	0.1173	0.0931	0.2257	-0.0383	0.0192	0.4895	0.0742	0.1094	4.6191	122.4272	13.9915

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 49:61)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 62:82)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 83:121)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 122:135)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 136:145)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 146:163)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 164:191)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 192:214)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 215:243)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 54:69)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 70:82)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 83:116)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 117:145)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 146:163)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 164:201)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 202:214)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 215:245)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 1:20)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 1:20)

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