PDB-4wyq: Crystal structure of the Dicer-TRBP interface

ID or keywords:

Entry

Database: PDB / ID: 4wyq

Title

Crystal structure of the Dicer-TRBP interface

Components

Endoribonuclease Dicer
Poly(UNK)
RISC-loading complex subunit TARBP2

Keywords

HYDROLASE/PROTEIN BINDING / RNA interference / microRNA / dsRBP / dsRBD / HYDROLASE-PROTEIN BINDING complex

Function / homology

Function and homology information

regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.2 Å

Authors

Wilson, R.C. / Doudna, J.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM073794	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM096689	United States

Citation

Journal: Mol.Cell / Year: 2015
Title: Dicer-TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis.
Authors: Wilson, R.C. / Tambe, A. / Kidwell, M.A. / Noland, C.L. / Schneider, C.P. / Doudna, J.A.

History

Deposition	Nov 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 21, 2015	Group: Database references
Revision 1.2	Feb 18, 2015	Group: Database references
Revision 1.3	Aug 26, 2015	Group: Other
Revision 1.4	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.classification
Revision 1.6	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wyq.cif.gz	172.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4wyq_validation.pdf.gz	453.6 KB	Display	wwPDB validaton report
Full document	4wyq_full_validation.pdf.gz	461.8 KB	Display
Data in XML	4wyq_validation.xml.gz	16.3 KB	Display
Data in CIF	4wyq_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wy/4wyq ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wyq	HTTPS FTP

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Related structure data

Similar structure data	4n2o-6 5hou-d 4znl-1 7ks4-d 5bua-d 4ese-d 3gyg-3 5hca-3 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
Related items in Molecule of the Month	#98 - Feb 2008 Small Interfering RNA similarity (12) #105 - Sep 2008 Ribonuclease A similarity (11) #205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: Endoribonuclease Dicer

B: RISC-loading complex subunit TARBP2

C: Poly(UNK)

D: Endoribonuclease Dicer

E: RISC-loading complex subunit TARBP2

F: Poly(UNK)

47 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Endoribonuclease Dicer

B: RISC-loading complex subunit TARBP2

C: Poly(UNK)

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

2

D: Endoribonuclease Dicer

E: RISC-loading complex subunit TARBP2

F: Poly(UNK)

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

Unit cell

Length a, b, c (Å)	291.910, 291.910, 291.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	210
Space group name H-M	F4₁32

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2
1	3
2	3

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 269:386) AND (NAME CA OR NAME C OR NAME N OR NAME O)
2	1	1	CHAIN D AND (RESSEQ 269:386) AND (NAME CA OR NAME C OR NAME N OR NAME O)
1	1	2	CHAIN B AND (RESSEQ 294:362) AND (NAME CA OR NAME C OR NAME N OR NAME O)
2	1	2	CHAIN E AND (RESSEQ 294:362) AND (NAME CA OR NAME C OR NAME N OR NAME O)
1	1	3	CHAIN F AND (NAME CA OR NAME C OR NAME N OR NAME O)
2	1	3	CHAIN C AND (NAME CA OR NAME C OR NAME N OR NAME O)

NCS ensembles :

ID
1
2
3

#1: Protein	Endoribonuclease Dicer / Helicase with RNase motif / Helicase MOI Mass: 14482.081 Da / Num. of mol.: 2 / Fragment: unp residues 267-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DICER1, DICER, HERNA, KIAA0928 / Plasmid: 2D Details (production host): plasmid for polycistronic expression Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9UPY3, ribonuclease III
#2: Protein	RISC-loading complex subunit TARBP2 / TAR RNA-binding protein 2 / Trans-activation-responsive RNA-binding protein Mass: 8076.228 Da / Num. of mol.: 2 / Fragment: unp residues 289-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TARBP2, TRBP / Plasmid: 2D Details (production host): plasmid for polycistronic expression Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q15633
#3: Protein/peptide	Poly(UNK) Mass: 954.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: 2D Details (production host): plasmid for polycistronic expression Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
Sequence details	Chains C and F represent TRBP residues for which residue identity could not be established. These ...Chains C and F represent TRBP residues for which residue identity could not be established. These residues were included since they are illuminating regarding the orientation of the portion of TRBP N-terminal to that represented in chains B and E.

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 5.51 Å³/Da / Density % sol: 77.68 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2 uL of 7.3 g/L protein solution in buffer [0.01 M sodium acetate, 0.05 M sodium chloride, 0.001 M TCEP, and 5% (w/v) glycerol] was mixed with 1 uL [18% PEG 3350 (w/v), 0.26 M potassium sulfate, 0.001 M TCEP].

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11111 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11111 Å / Relative weight: 1
Reflection	Resolution: 3.2→49.35 Å / Num. obs: 18119 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / R_sym value: 0.182 / Net I/σ(I): 18.55
Reflection shell	Resolution: 3.2→3.28 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.7.2_869)	refinement
XDS		data reduction
XDS		data scaling
SHELX		phasing
SOLVE		phasing
ARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 3.2→48.65 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	905	4.99 %	Random
R_work	0.228	-	-	-
obs	0.23	18119	99.9 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 71.92 Å² / k_sol: 0.31 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 3.2→48.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3192	0	0	0	3192

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	3236
X-RAY DIFFRACTION	f_angle_d	1.61	4358
X-RAY DIFFRACTION	f_dihedral_angle_d	18.718	1208
X-RAY DIFFRACTION	f_chiral_restr	0.117	514
X-RAY DIFFRACTION	f_plane_restr	0.008	550

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	456	X-RAY DIFFRACTION	POSITIONAL
1	2	D	456	X-RAY DIFFRACTION	POSITIONAL	0.078
2	1	B	276	X-RAY DIFFRACTION	POSITIONAL
2	2	E	276	X-RAY DIFFRACTION	POSITIONAL	0.044
3	1	F	44	X-RAY DIFFRACTION	POSITIONAL
3	2	C	44	X-RAY DIFFRACTION	POSITIONAL	0.044

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 (%)
3.2003-3.4007	0.3296	146	0.2987	2799	X-RAY DIFFRACTION	100
3.4007-3.6632	0.2839	147	0.2513	2795	X-RAY DIFFRACTION	100
3.6632-4.0317	0.228	149	0.2193	2821	X-RAY DIFFRACTION	100
4.0317-4.6147	0.2149	150	0.1912	2844	X-RAY DIFFRACTION	100
4.6147-5.8125	0.2648	151	0.2087	2884	X-RAY DIFFRACTION	100
5.8125-48.6573	0.2684	162	0.2375	3071	X-RAY DIFFRACTION	100

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	6.6347	5.6323	0.6732	5.5893	3.5251	2.0005	-0.6311	-1.0012	-0.7851	-0.0657	-0.6792	1.0072	1.9927	-1.4894	1.1158	0.5779	-0.0327	0.0869	0.7445	-0.1083	1.1432	26.415	53.916	-10.085
2	7.9559	-4.9166	1.8516	4.3034	-0.5651	2.2013	0.1128	1.3414	-0.45	-0.3157	0.2164	-0.8525	0.1506	0.3984	0.6319	0.1142	0.0604	-0.0428	1.2511	-0.504	0.9504	32.661	61.7	-14.149
3	8.732	-2.6851	-5.9591	5.8304	-0.5575	6.3467	0.0766	2.3787	-0.1988	-0.2584	0.3913	-1.189	-0.2174	0.5111	-0.2108	0.4468	-0.2803	-0.151	1.3608	0.1717	0.8621	33.389	68.962	-13.207
4	4.1102	1.8663	0.8098	3.788	1.4186	0.5356	0.0002	-0.5397	-0.9533	0.7833	-0.95	-0.4533	-0.2543	1.868	0.9747	0.637	0.0655	-0.2794	0.7141	0.0669	0.9264	32.795	59.275	4.992
5	1.1778	0.8526	0.9	9.1826	8.4999	8.1898	0.1226	-0.4199	-0.9241	0.6217	0.0845	0.7058	0.2751	-0.3088	-0.2897	0.5557	-0.0815	-0.0035	0.7209	0.4414	1.2607	24.876	53.409	9.977
6	8.3751	3.6965	-2.2204	9.8509	-5.4599	3.0326	-0.0646	0.1599	0.2929	-0.4462	0.238	-0.8466	0.0686	0.1461	0.1067	0.4528	-0.0384	0.0885	0.6954	-0.1991	0.7088	30.388	68.641	-2.99
7	4.2696	-0.8878	-0.9326	2.9973	-2.8581	3.5517	-0.0507	0.1391	-1.0366	0.3008	-0.9243	-0.4836	0.1381	0.2786	0.4782	0.0647	0.0375	-0.0812	0.5353	-0.2132	0.58	27.319	59.45	0.498
8	1.2112	-0.1719	0.4812	2.4103	-0.7842	1.464	0.2288	-0.1694	-0.6174	-0.0942	0.0527	0.4017	0.5817	-0.5967	-0.8478	0.0167	-0.1665	-0.3085	0.5744	-0.2807	0.5193	23.088	62.296	-6.902
9	5.7331	3.7426	3.3682	3.1795	1.2368	3.2363	0.306	0.3007	-0.9597	-0.5733	0.2076	1.3199	1.2611	-1.0153	-0.3885	1.0004	-0.3969	-0.2124	0.5686	-0.0678	1.2581	6.572	62.936	-1.747
10	6.5	0.1526	3.6757	8.9236	2.8855	8.0054	0.1875	-1.4251	-1.3675	0.2517	0.205	-0.8178	0.1115	0.5164	-0.3204	0.2712	-0.047	0.0314	0.7702	0.159	0.4301	19.144	65.919	10.562
11	3.0811	4.1823	-3.4722	8.7705	-4.4027	5.7706	-0.1046	0.6592	0.009	0.1239	0.0804	0.5671	-0.6482	-0.1065	-0.0051	0.1951	0.0424	-0.0365	0.5625	-0.0599	0.2973	8.378	76.475	2.777
12	4.6845	1.1686	0.2538	3.8772	0.5786	2.0114	0.4945	-0.3553	0.5809	0.445	0.0619	-0.6067	-0.2228	0.2945	-0.1325	0.1014	-0.312	0.0635	0.9176	0.0281	0.4785	23.841	74.148	4.088
13	2.4935	0.7876	0.3762	2.4604	0.3704	2.2253	-0.2418	-0.1931	-0.2043	0.0277	0.1455	-0.4884	-0.4726	0.8683	0.0898	-0.2762	-0.0212	-0.1024	0.6068	0.0626	0.2895	-1.81	79.752	-9.752
14	0.6604	-0.5907	0.0499	0.6656	0.2438	0.6028	0.0164	0.1281	0.7487	-0.2124	-0.0698	0.2265	-1.9609	-0.1342	-0.0034	1.6144	-0.0955	0.0039	0.8151	-0.0343	1.1888	14.257	100.043	41.979
15	3.8517	-1.4177	-0.0177	1.9228	-1.7636	2.2353	0.8195	-1.2457	1.8648	1.7083	0.9435	-2.307	-1.3286	1.196	-1.2261	1.8471	-0.3935	0.116	1.2012	-0.5114	1.1829	24.855	98.447	44.679
16	8.0337	2.3265	4.2152	1.8594	1.6511	4.6715	-0.126	-0.0761	0.5528	0.1056	-0.0086	-0.2453	-1.064	0.9958	-0.2763	1.6615	-1.0305	-0.46	1.6002	-0.3833	1.3079	30.182	93.175	43.85
17	3.4305	-2.5299	5.0055	6.967	-2.4372	7.8396	-0.3211	0.6831	2.5221	0.6954	-0.267	-0.4236	-2.2931	0.9711	0.5442	1.614	-0.3303	0.2369	1.1062	0.1182	1.2775	20.674	98.181	25.978
18	4.1324	2.8314	4.1193	2.4035	2.5412	4.2754	0.3968	-0.182	0.0231	1.0598	0.4281	0.4211	-0.5874	0.1141	-0.7258	1.281	0.2379	0.1433	0.9625	0.0703	1.0589	9.988	97.037	22.716
19	1.1481	1.1754	0.4025	2.4993	-0.8012	5.51	-0.427	0.396	0.4297	-0.4245	-0.2245	0.2479	-0.248	0.1895	0.7279	1.1885	-0.6087	0.0857	1.1717	-0.272	0.8426	25.975	90.331	34.121
20	4.7399	-4.4123	5.4844	4.1697	-5.1863	6.4445	-0.3337	-0.1909	1.3832	1.1325	-0.4224	-0.5332	-0.9898	-0.1255	0.5204	1.2637	-0.1818	-0.0231	0.7046	-0.1896	0.8149	17.133	95.223	31.43
21	1.1603	-1.2913	-0.2605	4.4437	-1.3083	0.9226	0.0502	-0.2873	0.5863	-0.1975	-0.2174	0.4353	-0.8983	-0.1469	0.932	1.1176	-0.4568	0.0498	0.6622	-0.6239	0.633	16.886	91.159	39.561
22	3.4187	3.1363	-2.4543	2.9032	-1.9889	4.4186	-0.4981	-1.2912	1.7386	2.4931	1.1834	1.6471	-1.0883	-1.2375	-0.7311	0.879	0.4754	0.1279	1.0231	0.0145	1.1665	4.391	79.453	37.997
23	2.7832	-0.7232	0.5805	8.2841	-1.5048	7.9433	-0.1663	0.6771	0.9293	-0.6828	0.6431	0.0823	-0.1329	0.0258	-0.5246	0.4067	-0.0249	-0.0884	0.7112	-0.0819	0.4551	13.537	83.99	22.9
24	7.2783	5.8746	-1.6163	8.8354	-1.4319	7.0357	0.2977	-0.0607	-0.9346	0.6301	-0.1069	-0.7276	0.5265	0.8641	-0.2232	0.4701	-0.0572	-0.1136	0.5425	-0.0572	0.387	14.071	69.754	32.313
25	3.3368	-1.7013	1.3428	2.6158	0.6293	4.1572	0.2135	0.8426	0.2692	-0.0097	-0.2178	-1.2698	-0.8217	0.8265	0.1577	0.4044	-0.6124	-0.1773	1.1215	-0.1376	0.8455	23.479	81.555	28.251
26	7.3533	1.6516	-6.0237	4.4983	-3.5142	7.0976	0.4777	-0.5577	0.0463	0.1884	-0.2129	0.0083	0.1365	1.3929	-0.0833	0.7012	-0.03	-0.2401	0.6707	-0.0178	0.5162	10.804	62.129	46.703
27	0.191	0.0611	0.3159	0.0189	0.1005	0.5203	-0.1981	0.1268	-0.0117	-0.8509	0.3424	0.0033	0.1071	-0.1214	0.051	0.6673	0.2116	0.3124	0.5734	0.4665	0.3908	24.221	69.449	-18.68
28	2.5452	-1.2311	-0.5053	2.0444	-2.1906	4.1884	0.2183	-0.673	0.0597	0.1519	0.0784	-0.0562	-0.7918	-0.0426	-0.0393	1.0005	0.0153	-0.3482	0.9259	-0.0324	0.2026	24.226	87.2	50.756

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN B AND RESID 289:295 )	B	289 - 295
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 296:303 )	B	296 - 303
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID 304:308 )	B	304 - 308
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 309:317 )	B	309 - 317
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 318:324 )	B	318 - 324
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 325:332 )	B	325 - 332
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 333:345 )	B	333 - 345
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 346:363 )	B	346 - 363
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 269:274 )	A	269 - 274
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 275:309 )	A	275 - 309
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 310:330 )	A	310 - 330
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 331:361 )	A	331 - 361
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 362:391 )	A	362 - 391
14	X-RAY DIFFRACTION	14	( CHAIN E AND RESID 289:295 )	E	289 - 295
15	X-RAY DIFFRACTION	15	( CHAIN E AND RESID 296:303 )	E	296 - 303
16	X-RAY DIFFRACTION	16	( CHAIN E AND RESID 304:308 )	E	304 - 308
17	X-RAY DIFFRACTION	17	( CHAIN E AND RESID 309:317 )	E	309 - 317
18	X-RAY DIFFRACTION	18	( CHAIN E AND RESID 318:324 )	E	318 - 324
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 325:332 )	E	325 - 332
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 333:345 )	E	333 - 345
21	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 346:363 )	E	346 - 363
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 269:274 )	D	269 - 274
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 275:309 )	D	275 - 309
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 310:330 )	D	310 - 330
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 331:361 )	D	331 - 361
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 362:391 )	D	362 - 391
27	X-RAY DIFFRACTION	27	( CHAIN C AND RESID 8:11 )	C	8 - 11
28	X-RAY DIFFRACTION	28	( CHAIN F AND RESID 8:11 )	F	8 - 11

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