PDB-5n96: Crystal Structure of Drosophila DHX36 helicase in complex with AG...

ID or keywords:

Entry

Database: PDB / ID: 5n96

Title

Crystal Structure of Drosophila DHX36 helicase in complex with AGGGTTTTTT

Components

CG9323, isoform A
DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')

Keywords

HYDROLASE / Helicase DExH ssDNA

Function / homology

Function and homology information

DEx/H-box helicases activate type I IFN and inflammatory cytokines production / G-quadruplex DNA unwinding / G-quadruplex DNA binding /

DNA helicase activity /

helicase activity / G-quadruplex RNA binding /

RNA helicase activity /

RNA helicase /

hydrolase activity /

ATP binding ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.716 Å

Authors

Chen, W.-F. / Rety, S. / Guo, H.-L. / Wu, W.-Q. / Liu, N.-N. / Liu, Q.-W. / Dai, Y.-X. / Xi, X.-G.

Citation

Journal: Structure / Year: 2018
Title: Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.
Authors: Chen, W.F. / Rety, S. / Guo, H.L. / Dai, Y.X. / Wu, W.Q. / Liu, N.N. / Auguin, D. / Liu, Q.W. / Hou, X.M. / Dou, S.X. / Xi, X.G.

History

Deposition	Feb 24, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Advisory / Data collection / Derived calculations Category: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2	Jan 17, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5n96.cif.gz	716.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n9/5n96 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/5n96	HTTPS FTP

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Related structure data

Related structure data	5n8rSC 5n8sC 5n90C 5n94C 5n98C 5n9aC 5n9dC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5n90-2 5n9e-1 5n8r-2 5n9a-1 5n8z-1 5n90-1 5n9f-1 5n9d-1 5n9e-2 5n94-2 5n8z-2 5n9f-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: CG9323, isoform A

B: CG9323, isoform A

C: DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')

D: DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')

hetero molecules

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

1

A: CG9323, isoform A

C: DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')

hetero molecules

defined by author&software
Evidence: SAXS
112 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CG9323, isoform A

D: DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')

hetero molecules

defined by author&software
112 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	303.389, 51.316, 164.602
Angle α, β, γ (deg.)	90.00, 114.57, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	CG9323, isoform A / CG9323 / isoform B / GH12763p Mass: 108401.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9323, Dmel_CG9323 / Plasmid: pTwin1 / Production host: Escherichia coli (E. coli) / Variant (production host): C2566H / References: UniProt: Q8SWT2, EC: 3.6.1.3
#2: DNA chain	DNA (5'-D(PAPGPGPGPTPTPTPTPTPT)-3') Mass: 3081.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.69 Å³/Da / Density meas: 54.3 Mg/m³ / Density % sol: 52.93 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES monohydrate-imidazole 20mM sodium formate 20mM ammonium acetate 20mM sodium citrate tribasic hydrate 20mM sodium oxamate 20mM potassium sodium tartrate tetrahydrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.716→56.65 Å / Num. obs: 61776 / % possible obs: 97.57 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / B_iso Wilson estimate: 50.38 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.1022 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.716→2.813 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.7207 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 6222 / CC_1/2: 0.778 / % possible all: 99.86

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2427: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5N8R

5n8r

Resolution: 2.716→56.65 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.01

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2481	3130	5.07 %	5%
R_work	0.1797	-	-	-
obs	0.1832	61759	97.58 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.716→56.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13643	382	2	129	14156

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	14307
X-RAY DIFFRACTION	f_angle_d	1.409	19385
X-RAY DIFFRACTION	f_dihedral_angle_d	16.655	8808
X-RAY DIFFRACTION	f_chiral_restr	0.074	2179
X-RAY DIFFRACTION	f_plane_restr	0.009	2441

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 (%)
2.7162-2.7587	0.3497	147	0.2775	2651	X-RAY DIFFRACTION	100
2.7587-2.8039	0.3758	137	0.2625	2715	X-RAY DIFFRACTION	100
2.8039-2.8523	0.3124	134	0.2448	2764	X-RAY DIFFRACTION	100
2.8523-2.9041	0.3347	142	0.2509	2623	X-RAY DIFFRACTION	100
2.9041-2.96	0.3173	154	0.246	2691	X-RAY DIFFRACTION	100
2.96-3.0204	0.3033	150	0.2451	2745	X-RAY DIFFRACTION	100
3.0204-3.0861	0.2978	131	0.2349	2672	X-RAY DIFFRACTION	100
3.0861-3.1579	0.3563	133	0.2341	2699	X-RAY DIFFRACTION	100
3.1579-3.2368	0.3355	146	0.2302	2752	X-RAY DIFFRACTION	100
3.2368-3.3244	0.2553	122	0.2131	2677	X-RAY DIFFRACTION	100
3.3244-3.4222	0.3049	175	0.2063	2739	X-RAY DIFFRACTION	100
3.4222-3.5326	0.2999	88	0.2	2119	X-RAY DIFFRACTION	79
3.5326-3.6589	0.2526	129	0.2011	2454	X-RAY DIFFRACTION	96
3.6589-3.8054	0.2603	141	0.1789	2465	X-RAY DIFFRACTION	98
3.8054-3.9785	0.2487	139	0.1602	2550	X-RAY DIFFRACTION	93
3.9785-4.1882	0.2042	149	0.1444	2695	X-RAY DIFFRACTION	100
4.1882-4.4506	0.2118	167	0.1326	2707	X-RAY DIFFRACTION	100
4.4506-4.7941	0.1843	147	0.1288	2755	X-RAY DIFFRACTION	100
4.7941-5.2764	0.2087	144	0.1393	2746	X-RAY DIFFRACTION	100
5.2764-6.0395	0.2646	148	0.1681	2753	X-RAY DIFFRACTION	100
6.0395-7.6074	0.222	158	0.1717	2779	X-RAY DIFFRACTION	99
7.6074-66.3062	0.1802	149	0.1544	2878	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	1.0917	0.0868	-0.0857	0.77	-0.44	2.9575	0.1287	-0.4136	-0.109	0.1237	0.006	0.0733	0.1821	-0.2901	-0.1505	0.3011	-0.1199	-0.003	0.348	-0.0228	0.3244	-54.572	-17.1242	51.1921
2	2.662	-0.5933	-0.4822	0.7397	0.0551	1.4792	0.0243	-0.3499	-0.1387	0.0375	-0.0496	-0.2138	0.0661	0.4527	0.0426	0.3916	-0.1108	-0.0918	0.4867	0.0404	0.4393	-23.8728	-17.7549	52.4391
3	1.0772	-0.1098	-0.1934	0.9429	0.1232	1.8085	0.0543	0.0694	0.067	-0.0672	-0.0753	-0.196	-0.2012	0.0892	0.0225	0.4092	-0.0714	0.0086	0.2475	0.0195	0.318	-41.9706	-8.9281	22.6045
4	1.2283	-0.0464	0.6286	0.5618	0.6992	3.8253	0.1429	0.1621	-0.1612	-0.1041	0.1034	-0.1027	0.3836	1.0354	-0.2646	0.4369	0.0492	-0.0015	0.4263	-0.0104	0.3616	-87.364	-35.8312	29.8609
5	3.1982	0.6794	-0.1049	1.1688	0.6761	2.0647	0.248	-0.8348	0.4976	0.0112	-0.1592	0.1975	-0.595	0.2054	-0.0487	0.4914	-0.1583	0.0833	0.748	-0.1326	0.3763	-93.3531	-10.6653	70.3524
6	1.8398	0.0942	0.4951	2.0705	0.2412	2.4233	-0.0076	-0.4925	0.1701	0.0135	0.0197	0.0603	-0.3642	0.3097	-0.0246	0.3267	-0.0951	0.1149	0.4351	-0.0265	0.2929	-95.2647	-18.4512	55.6517
7	2.118	-0.4157	-0.6332	1.0126	0.4008	1.8286	-0.0623	-0.4062	-0.0496	-0.1442	0.0321	0.3708	-0.3728	-0.6376	0.009	0.3557	0.058	-0.0018	0.6444	0.0134	0.4467	-130.0771	-18.2459	59.8568
8	3.0014	-1.8253	-0.6702	1.4085	1.4034	2.4603	0.0545	-0.3719	0.0737	-0.4203	-0.0446	0.0394	-0.39	-0.3274	-0.0023	0.349	-0.0023	0.0417	0.4312	0.0604	0.3223	-120.481	-19.8986	52.6839
9	2.1813	0.0517	-1.0502	0.9387	-0.2906	4.6743	-0.0033	-0.1386	-0.3023	-0.2784	0.0817	0.1593	0.6878	0.1222	-0.1272	0.421	-0.0367	-0.0332	0.1934	0.0097	0.4361	-100.0687	-38.5313	38.9359
10	2.1091	-0.3212	0.3523	1.4177	0.0563	1.8887	0.0126	0.0441	0.0849	-0.1529	0.0099	0.1372	-0.2908	-0.1886	-0.0255	0.5723	-0.0141	0.0306	0.2365	0.0219	0.2976	-112.0741	-21.2251	25.364
11	3.495	-0.0881	0.8082	1.2628	0.3473	3.459	0.302	0.2783	-0.2855	-0.3818	-0.109	0.1056	0.4549	0.1998	-0.2328	0.6761	0.0463	-0.0274	0.2676	-0.0601	0.3209	-101.4389	-39.1928	13.4435
12	7.0741	-1.1566	-1.4077	2.1426	0.5116	3.1202	0.2276	-0.5288	-0.1403	-0.2097	-0.2755	-0.4401	-0.0195	0.1652	-0.0158	0.4948	-0.1148	-0.037	0.3164	0.0012	0.4545	-33.1797	-16.2372	37.2335
13	8.0348	-0.7251	0.8248	2.1884	-0.2288	2.5379	-0.1197	0.264	-0.298	-0.0149	-0.1564	0.2254	0.0704	0.1509	0.2383	0.4431	-0.0202	0.0685	0.2969	0.0554	0.3996	-114.979	-21.2552	40.4801

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 52 through 264 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 265 through 584 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 585 through 929 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 54 through 123 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 124 through 196 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 197 through 300 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 301 through 462 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 463 through 584 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 585 through 649 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 650 through 852 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 853 through 929 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 11 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 11 )

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