PDB-4x8w: dsRBD3 of Loquacious

ID or keywords:

Entry

Database: PDB / ID: 4x8w

Title

dsRBD3 of Loquacious

Components

Loquacious
Loquacious, isoform B

Keywords

GENE REGULATION / double stranded RNA binding domain / dimerization / dicer binding / miRNA processing

Function / homology

Function and homology information

MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / PKR-mediated signaling / regulation of regulatory ncRNA processing / dosage compensation by hyperactivation of X chromosome / RISC complex binding / germ-line stem cell population maintenance / RISC-loading complex / miRNA metabolic process ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.647 Å

Authors

Jakob, L. / Treiber, N. / Treiber, T. / Stotz, M. / Meister, G.

Citation

Journal: To Be Published
Title: Structure of the dsRBD3 of Loquacious reveals features for dimerization and Dicer1-interaction
Authors: Jakob, L. / Treiber, T. / Treiber, N. / Stotz, M. / Meister, G.

History

Deposition	Dec 10, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x8w.cif.gz	188.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4x8w.ent.gz	161.3 KB	Display	PDB format
PDBx/mmJSON format	4x8w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x8w_validation.pdf.gz	499.3 KB	Display	wwPDB validaton report
Full document	4x8w_full_validation.pdf.gz	506.1 KB	Display
Data in XML	4x8w_validation.xml.gz	19.3 KB	Display
Data in CIF	4x8w_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8w ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8w	HTTPS FTP

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Related structure data

Similar structure data	3vkl-2 3vkl-1 3e2m-d 2frs-d 4j32-d 3fiq-d 6rsk-d 1qc5-d 2ygn-1 6fs2-d Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#105 - Sep 2008 Ribonuclease A similarity (4)

Deposited unit

A: Loquacious, isoform B

B: Loquacious, isoform B

C: Loquacious, isoform B

D: Loquacious, isoform B

E: Loquacious, isoform B

F: Loquacious, isoform B

G: Loquacious, isoform B

H: Loquacious

hetero molecules

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

1

A: Loquacious, isoform B

B: Loquacious, isoform B

D: Loquacious, isoform B

E: Loquacious, isoform B

hetero molecules

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

2

C: Loquacious, isoform B

F: Loquacious, isoform B

G: Loquacious, isoform B

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

3

H: Loquacious

defined by software
3.43 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.018, 112.970, 114.049
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Loquacious, isoform B / R3D1-L / RE14437p Mass: 8175.219 Da / Num. of mol.: 7 / Fragment: UNP RESIDUES 392-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: loqs, CG6866, Dmel_CG6866 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VJY9
#2: Protein/peptide	Loquacious Mass: 3429.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: fragments of loquacious with insufficient electron density Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Loquacious / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% PEG1000 12% PEG8000 50 mM Hepes-NaOH 250 mM NaCl 1mM DTT

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.647→50 Å / Num. obs: 25522 / % possible obs: 99.9 % / Redundancy: 7.4 % / R_sym value: 0.046 / Net I/σ(I): 33.8
Reflection shell	Resolution: 2.65→2.81 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.035 / Mean I/σ(I) obs: 6 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
Coot		model building
XDS		data reduction
SHARP		phasing
XSCALE		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.647→25.453 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.251	2482	5.18 %	Random selection
R_work	0.206	-	-	-
obs	0.2084	25451	99.75 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.647→25.453 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3626	0	6	67	3699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3679
X-RAY DIFFRACTION	f_angle_d	1.2	4994
X-RAY DIFFRACTION	f_dihedral_angle_d	15.397	1265
X-RAY DIFFRACTION	f_chiral_restr	0.054	590
X-RAY DIFFRACTION	f_plane_restr	0.006	643

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 (%)
2.6468-2.6976	0.3073	99	0.2636	2534	X-RAY DIFFRACTION	99
2.6976-2.7526	0.29	138	0.2495	2575	X-RAY DIFFRACTION	100
2.7526-2.8124	0.3088	142	0.2511	2485	X-RAY DIFFRACTION	100
2.8124-2.8778	0.2947	162	0.2401	2510	X-RAY DIFFRACTION	100
2.8778-2.9496	0.2835	124	0.2502	2524	X-RAY DIFFRACTION	100
2.9496-3.0293	0.2893	163	0.2283	2520	X-RAY DIFFRACTION	100
3.0293-3.1182	0.2699	135	0.2107	2546	X-RAY DIFFRACTION	100
3.1182-3.2187	0.2911	141	0.2279	2524	X-RAY DIFFRACTION	100
3.2187-3.3335	0.2735	127	0.222	2537	X-RAY DIFFRACTION	100
3.3335-3.4667	0.27	150	0.2107	2541	X-RAY DIFFRACTION	100
3.4667-3.624	0.267	110	0.2135	2529	X-RAY DIFFRACTION	100
3.624-3.8145	0.2941	149	0.2116	2502	X-RAY DIFFRACTION	100
3.8145-4.0526	0.2469	133	0.2085	2538	X-RAY DIFFRACTION	100
4.0526-4.364	0.2764	126	0.1863	2563	X-RAY DIFFRACTION	100
4.364-4.8006	0.2229	147	0.1723	2485	X-RAY DIFFRACTION	100
4.8006-5.4891	0.2203	164	0.1822	2521	X-RAY DIFFRACTION	100
5.4891-6.8929	0.2025	160	0.2146	2496	X-RAY DIFFRACTION	100
6.8929-25.4545	0.1921	112	0.1838	2463	X-RAY DIFFRACTION	97

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	0.4782	0.0474	-0.0219	0.2952	-0.2442	0.2958	0.38	-0.2071	0.4882	0.1291	-0.4379	-0.37	-0.2914	0.1627	-0.25	0.4498	-0.0929	0.0536	0.3137	0.0025	0.688	8.6006	36.8572	44.9117
2	0.0021	-0.0082	-0.0017	0.0834	0.0572	0.0466	-0.0365	-0.0292	-0.0311	-0.4016	-0.1821	0.4173	-0.0149	0.2689	-0.0056	0.364	-0.0067	0.1811	0.4478	0.0578	1.0548	-3.8217	33.469	35.8666
3	0.1768	0.0769	-0.0667	0.181	-0.2296	0.4673	-0.2091	0.0764	0.021	-0.3298	0.0758	0.1067	0.1544	0.1875	-0.2445	0.4424	-0.0085	-0.0895	0.3349	0.0979	0.4974	24.5304	44.5278	21.1003
4	0.5341	0.0777	0.0619	1.0329	0.0398	0.3341	-0.0369	0.2839	0.1542	-0.4328	0.058	0.6653	-0.0109	-0.0552	-0.0772	0.334	0.0086	-0.0365	0.2128	0.0774	0.4848	19.741	45.296	21.7291
5	0.1332	0.0875	0.0528	0.1641	0.0473	0.0273	0.0358	0.0833	0.4265	0.5219	0.0356	-0.1527	-0.1499	0.0701	-0.0029	0.3979	-0.0673	0.1248	0.3841	-0.0868	0.6651	3.7968	30.8308	42.6722
6	0.2108	0.164	0.2054	0.2841	0.0676	0.2474	0.4866	0.0913	0.3536	-0.0732	-0.088	-0.1552	-0.253	0.043	0.2751	0.3225	0.0624	0.246	0.4079	0.0156	0.5159	46.1707	24.2448	27.38
7	0.0483	0.1566	-0.2177	0.4962	-0.6821	0.9833	0.2686	0.1953	-0.0019	-0.0847	0.2472	-0.1776	0.0023	-0.3546	0.2495	0.217	-0.0347	-0.0212	0.4025	-0.3254	-0.0684	39.0947	15.0081	29.0946
8	0.0152	0.0012	-0.024	0.0224	0.0069	0.0241	0.1504	-0.0291	0.1391	0.0535	-0.1202	0.066	0.051	0.0732	-0.0001	0.4246	0.0372	0.0252	0.5129	-0.0477	0.6337	20.211	22.8676	33.3307
9	0.3054	0.1134	-0.0142	0.1345	-0.0849	0.0847	0.0349	-0.0851	-0.0185	-0.1628	-0.0377	-0.1945	-0.1602	0.1972	-0.0917	0.3291	0.0193	0.0206	0.3613	-0.0849	0.21	37.134	15.5399	34.2065
10	0.2941	0.0617	-0.1192	0.2038	0.162	0.2305	0.2128	0.0877	0.236	-0.0738	0.0776	0.0182	-0.2391	0.0828	0.7568	0.3743	0.0081	0.191	0.2405	-0.0608	0.0414	31.4118	22.8061	33.5381
11	0.8897	0.2674	0.0855	0.0968	-0.0589	0.6706	0.3498	0.0192	0.6829	0.0305	0.0009	-0.1118	-0.2122	0.1446	0.7261	0.2661	0.0058	0.0856	0.3856	-0.1589	0.3921	38.9099	24.5928	34.2368
12	0.1092	-0.072	0.1584	0.7301	-0.0584	0.2403	-0.0718	-0.2023	0.0189	0.3677	0.1419	0.2655	0.1178	-0.5513	0.1251	0.5332	-0.038	0.1124	0.6839	-0.0961	0.3714	23.7035	10.9937	48.7455
13	0.158	-0.0752	0.0478	0.0416	-0.0539	0.2567	0.1982	-0.227	-0.0313	0.0028	0.1198	-0.0386	0.1344	0.1804	0.3789	0.7119	0.1756	-0.058	0.6731	-0.2545	-0.1942	35.4148	11.7934	50.2413
14	0.3874	0.0453	-0.064	0.1774	-0.1317	0.1032	-0.0477	-0.5339	0.2672	0.2909	0.057	-0.0778	-0.2127	0.1151	-0.1749	0.4946	0.0367	0.0052	0.3615	-0.1054	0.225	38.9113	21.5563	46.7762
15	0.0035	-0.0075	-0.0113	0.0062	0.0185	0.0304	-0.0672	-0.0796	0.0618	0.2171	0.1211	-0.1634	-0.0532	0.1689	0.2496	0.3993	0.088	-0.5746	0.46	-0.0369	0.3908	39.8649	52.7161	34.2965
16	0.0087	0.0233	0.0025	0.0411	0.0114	0.042	0.0539	-0.169	0.0683	0.0281	-0.1051	-0.2976	0.069	0.043	0.0001	0.3768	0.1376	-0.0741	0.4105	0.0441	0.5691	38.2321	42.7445	30.2815
17	0.0005	0.0022	0.01	0.0016	0.0008	0.0214	0.0269	0.3754	-0.1861	-0.2393	-0.0044	-0.1673	-0.005	0.016	0.0003	0.8241	0.0579	-0.0601	0.61	0.0217	0.4748	35.0441	44.6291	10.3002
18	0.0121	-0.0153	-0.0433	0.2715	0.0566	0.0224	0.0337	-0.1783	-0.1199	-0.2384	0.0021	-0.374	0.1338	0.011	0.0314	0.488	0.0174	-0.0129	0.4069	0.1289	0.4226	33.6138	45.1448	24.4375
19	0.0359	-0.051	0.0182	0.0822	-0.0142	0.0191	0.1796	0.001	0.0354	0.1379	-0.0167	-0.3084	-0.184	0.044	-0.0001	0.4272	-0.0449	0.0403	0.3836	0.1012	0.3082	33.3723	52.4624	27.5243
20	0.0156	-0.0159	0.0177	0.011	-0.0115	0.0137	0.2087	0.0923	-0.1978	0.2054	-0.0896	0.1426	0.4703	0.1209	-0.0002	0.3814	-0.0469	-0.0343	0.3953	-0.1639	0.3522	-6.1222	13.4511	33.1118
21	0.0755	0.1503	0.0262	0.2897	0.0484	0.0084	0.2199	0.4051	-0.0019	0.1897	-0.3278	-0.4636	0.0679	0.0154	-0.0037	0.3703	0.0714	0.0106	0.4987	-0.0191	0.3249	4.0584	15.6359	35.934
22	0.4099	-0.4166	0.1111	0.9862	0.0514	0.0728	0.1394	-0.069	0.0335	0.2242	-0.1618	-0.3579	0.6749	-0.093	-0.144	0.4196	-0.0884	-0.0248	0.446	-0.1326	0.2925	1.6091	22.321	46.4768
23	0.4101	-0.4447	0.1268	0.5098	-0.1251	0.0418	0.186	0.0439	0.0543	0.0469	-0.5763	0.2719	0.1154	-0.1732	-0.0678	0.3409	-0.0595	0.0008	0.4617	-0.1353	0.3707	-4.8178	21.7419	38.2783
24	0.1334	0.0755	0.0475	0.0348	0.0218	0.0076	0.2388	-0.4116	0.1107	0.3191	-0.3175	-0.0808	0.2593	-0.1783	-0.0008	0.4083	-0.0453	-0.0405	0.3521	-0.1108	0.3351	38.3503	14.4422	45.7655
25	0.7037	0.2062	-0.0696	0.971	-0.1512	1.7516	-0.0902	0.1964	0.1816	-0.1454	0.1947	0.2163	-0.0127	-0.5395	0.5601	0.3638	0.0085	0.067	0.4732	-0.1027	0.3084	29.0181	16.0972	42.1457

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'E' and (resid 389 through 414 )
2	X-RAY DIFFRACTION	2	chain 'E' and (resid 415 through 431 )
3	X-RAY DIFFRACTION	3	chain 'E' and (resid 432 through 463 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 391 through 431 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 432 through 463 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 391 through 405 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 406 through 414 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 415 through 422 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 423 through 434 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 435 through 443 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 444 through 462 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 390 through 405 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 406 through 414 )
14	X-RAY DIFFRACTION	14	chain 'G' and (resid 415 through 433 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 392 through 405 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 406 through 413 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 414 through 422 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 423 through 443 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 444 through 463 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 391 through 404 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 405 through 413 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 414 through 443 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 444 through 462 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 429 through 443 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 444 through 463 )

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Yorodumi