PDB-4yhw: Yeast Prp3 (296-469) in complex with fragment of U4/U6 di-snRNA

ID or keywords:

Entry

Database: PDB / ID: 4yhw

Title

Yeast Prp3 (296-469) in complex with fragment of U4/U6 di-snRNA

Components

U4 snRNA fragment
U4/U6 small nuclear ribonucleoprotein PRP3
U6 snRNA fragment

Keywords

SPLICING / U4/U6 di-snRNP / RNA-protein complex

Function / homology

Function and homology information

U4/U6 snRNP / U4 snRNP / spliceosomal complex assembly / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex /

spliceosomal complex /

mRNA splicing, via spliceosome /

nucleus
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.25 Å

Authors

Liu, S. / Wahl, M.C.

Funding support

Germany, 1items

Citation

Journal: Elife / Year: 2015
Title: A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing.
Authors: Liu, S. / Mozaffari-Jovin, S. / Wollenhaupt, J. / Santos, K.F. / Theuser, M. / Dunin-Horkawicz, S. / Fabrizio, P. / Bujnicki, J.M. / Luhrmann, R. / Wahl, M.C.

History

Deposition	Feb 27, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.inclination / _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yhw.cif.gz	225.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4yhw.ent.gz	180 KB	Display	PDB format
PDBx/mmJSON format	4yhw.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/yh/4yhw ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yhw	HTTPS FTP

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Related structure data

Related structure data	4yhuSC 4yhvC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2fnj-d 3m5m-d 6hxy-d 5hzo-d 1pbw-d 6b1x-d 3zx7-d 1xk9-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) 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	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #10 - Oct 2000 Ribosome similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #227 - Nov 2018 Telomerase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: U4/U6 small nuclear ribonucleoprotein PRP3

B: U4/U6 small nuclear ribonucleoprotein PRP3

C: U4 snRNA fragment

D: U4 snRNA fragment

E: U6 snRNA fragment

F: U6 snRNA fragment

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

1

A: U4/U6 small nuclear ribonucleoprotein PRP3

C: U4 snRNA fragment

E: U6 snRNA fragment

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

2

B: U4/U6 small nuclear ribonucleoprotein PRP3

D: U4 snRNA fragment

F: U6 snRNA fragment

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

Unit cell

Length a, b, c (Å)	144.672, 59.565, 109.783
Angle α, β, γ (deg.)	90.00, 118.52, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor 3 Mass: 21366.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PRP3, RNA3, YDR473C, D8035.16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03338
#2: RNA chain	U4 snRNA fragment Mass: 5427.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: RNA chain	U6 snRNA fragment Mass: 8548.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium fluoride 0.18 M DL-malic acid, pH 6.8 13.2 % PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97968 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 23, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97968 Å / Relative weight: 1
Reflection	Resolution: 3.25→30 Å / Num. obs: 24895 / % possible obs: 97.9 % / Redundancy: 2 % / R_merge(I) obs: 0.013 / Net I/σ(I): 5.38
Reflection shell	Resolution: 3.25→3.33 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.106 / Mean I/σ(I) obs: 0.9 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YHU

4yhu

Resolution: 3.25→29.782 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 33.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2993	1250	5.02 %
R_work	0.2485	-	-
obs	0.251	24894	98.31 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.25→29.782 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2206	1858	0	0	4064

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4338
X-RAY DIFFRACTION	f_angle_d	1.006	6252
X-RAY DIFFRACTION	f_dihedral_angle_d	14.326	1904
X-RAY DIFFRACTION	f_chiral_restr	0.054	755
X-RAY DIFFRACTION	f_plane_restr	0.006	473

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 (%)
3.2501-3.38	0.3886	135	0.3686	2631	X-RAY DIFFRACTION	98
3.38-3.5336	0.2928	140	0.3149	2619	X-RAY DIFFRACTION	98
3.5336-3.7196	0.4275	141	0.2978	2673	X-RAY DIFFRACTION	99
3.7196-3.9522	0.3669	134	0.2762	2640	X-RAY DIFFRACTION	99
3.9522-4.2565	0.2408	144	0.2131	2638	X-RAY DIFFRACTION	99
4.2565-4.6834	0.2768	140	0.202	2624	X-RAY DIFFRACTION	99
4.6834-5.3577	0.2207	143	0.1806	2666	X-RAY DIFFRACTION	99
5.3577-6.7372	0.2871	136	0.2644	2621	X-RAY DIFFRACTION	98
6.7372-29.7837	0.3054	137	0.2391	2532	X-RAY DIFFRACTION	95

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	5.1106	-2.0505	-0.9854	2.2239	-0.2291	3.0844	-0.109	0.1624	-0.0486	0.2387	0.0432	0.1513	-0.0217	-0.0396	-0.1	0.4179	0.0734	0.2892	0.3781	0.2498	0.5185	98.3028	7.9931	14.8143
2	3.8537	-1.3381	-1.6387	2.8188	0.7032	1.075	-0.0179	-0.1504	0.2499	0.25	0.0148	0.2294	-0.0804	0.0045	-0.0267	0.4112	0.4695	0.2098	0.497	-0.3945	0.3629	90.5628	17.5845	17.6329
3	1.8013	-0.406	-0.2176	0.9395	0.6655	1.0434	-0.3803	-0.4836	0.0664	0.5349	0.0141	0.7166	0.1874	-0.3383	0.1719	0.5635	0.2893	0.5603	0.2999	-0.2001	0.6282	94.7253	8.9713	19.401
4	2.4861	-2.0863	-0.2428	2.4872	0.8322	0.584	-0.4286	-0.5074	-0.8534	0.5637	-0.221	1.2172	0.1506	-0.3216	0.2872	0.7846	0.1989	0.3025	0.7308	0.1549	0.9182	85.44	5.8497	16.7866
5	1.652	1.7811	-0.8028	2.5879	-1.1791	0.6154	0.0716	0.0026	-0.2217	-0.033	0.1003	-0.3883	-0.0253	0.0644	0.0528	0.2944	-0.0075	0.0121	0.3044	-0.0343	1.1673	101.7428	2.8507	5.3788
6	0.2215	-1.1167	0.3067	6.2416	0.0344	4.8375	-0.1267	0.2388	0.3509	0.5532	0.4833	-0.3839	0.0544	0.0956	-0.1215	0.5384	0.1036	-0.0025	0.3757	0.0099	0.1547	117.6136	-4.0731	15.1479
7	1.2688	-1.8721	-0.4044	4.6867	-0.1251	1.3736	-0.1525	-0.1154	-0.2418	0.4659	0.1668	0.0915	0.0615	-0.0722	-0.1329	0.594	0.2829	-0.1558	0.3678	0.0749	0.9652	126.1845	-13.3803	17.9139
8	4.4198	-1.3518	0.1775	2.1596	0.476	2.6357	-0.2844	-0.454	-0.3861	0.4779	-0.1439	-0.6651	0.0649	0.1468	0.2405	0.4607	-0.1065	-0.1455	0.4058	0.0847	0.2498	121.3924	-6.0775	11.3987
9	2.3268	0.2268	0.3142	2.1666	-1.057	1.8043	-0.0816	-0.5531	-0.1678	0.5123	-0.0316	-0.4683	-0.1286	0.1597	-0.1029	0.8521	0.151	-0.2204	0.477	0.2462	0.4074	121.4025	-5.1433	24.3429
10	6.3103	-2.4536	-0.0928	4.0784	0.1617	3.0885	-0.2711	-0.1713	0.1794	0.2062	0.2204	-0.9365	0.3106	0.7711	0.1468	0.712	0.328	-0.3766	0.9347	0.1297	1.8019	140.659	-2.5407	17.4011
11	2.6307	-2.1623	0.3247	1.901	-0.578	1.3762	-0.4776	0.2814	-0.0588	0.1359	-0.0213	-0.0979	0.2007	0.2226	0.2663	0.3615	0.0789	0.057	0.1922	0.1551	0.9339	116.8856	-4.4681	7.1172
12	2.0746	1.16	1.2909	1.6055	1.6005	1.6846	-0.0028	-0.2493	-0.1834	-0.0368	0.3072	0.2154	0.2138	-0.1986	0.0716	0.2176	-0.0155	-0.0985	0.4448	0.1024	0.668	115.1912	1.2925	5.5584
13	0.0433	0.0256	0.0311	0.0595	0.0213	0.0016	0.309	-0.256	0.5994	0.2236	-0.335	0.0965	-0.3654	0.2116	-0.0005	3.4954	1.2516	-0.101	2.9962	-0.1608	3.8244	90.6309	51.6802	40.6479
14	0.0493	-0.0165	0.0248	0.0252	0.0368	0.0589	-0.6723	0.0774	-0.4232	0.4235	-0.0778	-0.1439	0.8823	-0.1441	-0.0004	2.5084	0.0658	0.0366	1.944	0.3118	1.7349	126.6393	-49.6037	39.912
15	0.045	0.0177	-0.0535	0.0446	-0.062	0.0749	-0.1947	0.3479	0.4082	0.0032	-0.2551	0.1639	-0.0393	0.273	-0.0006	2.7991	0.1671	0.8811	2.9823	-0.1596	3.4708	93.9936	50.4909	39.3477
16	0.0785	-0.1557	-0.0704	0.2525	0.1099	0.0656	-0.0486	-0.1103	0.1415	0.2088	0.1394	0.1384	-0.0496	-0.0414	0.3278	-0.234	0.5796	0.3813	-0.3084	-0.2038	0.1935	89.7735	21.2625	10.5238
17	0.038	0.0235	-0.0335	0.009	-0.0133	0.0377	-0.1986	-0.3372	0.0062	-0.239	-0.076	-0.1801	-0.2102	-0.0326	0.0002	2.8642	0.2624	0.1305	1.9829	0.2322	1.6829	125.8852	-48.6543	36.232
18	0.0496	-0.0756	0.0387	0.0886	-0.0458	0.0223	-0.0496	-0.0532	-0.0396	0.1427	0.0433	-0.1192	0.0521	0.0479	-0.2353	0.0629	0.5272	-0.0599	0.1169	-0.0848	0.4712	128.1827	-17.3519	11.0579
19	2.4053	-1.6264	-1.1552	3.2937	3.0947	6.6244	-0.1734	-0.0467	0.0764	0.0183	0.0557	-0.0253	-0.0936	-0.0613	-0.3235	0.3114	0.1787	0.0639	0.4279	-0.0149	0.1913	97.7676	14.0792	11.8196
20	1.1927	0.6193	1.5841	1.1679	-0.3147	4.887	-0.0367	0.3753	-0.0673	-0.191	-0.0026	-1.0272	-0.0809	0.431	-0.006	0.5927	-0.0816	0.1174	0.3181	0.0194	0.8357	108.4535	14.9899	6.4572
21	2.85	-1.9721	-2.2448	5.0301	1.41	3.3083	-0.3286	0.3267	-0.9549	-0.2875	-0.1928	-0.3017	-0.1297	-0.2866	-0.0082	0.2788	0.0181	0.0623	0.3076	-0.0673	0.4356	94.5286	8.3736	2.3521
22	0.0201	-0.0137	-0.0043	0.007	0.0033	0.0015	-0.1228	-0.1335	0.0936	0.7503	-0.2768	-0.5897	-0.2913	0.1168	-0.0026	1.1222	-0.0341	0.0496	1.1681	-0.1531	1.111	92.7571	23.5127	31.5616
23	0.0088	0.0137	0.0174	0.0172	0.0188	0.0278	-0.0133	0.0155	0.0204	0.0032	-0.062	-0.0086	-0.0231	0.0525	-0.2103	0.6502	0.4054	-0.426	0.6544	0.3137	0.4802	125.4933	-22.4104	28.4913

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 335 through 349 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 350 through 362 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 372 through 405 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 406 through 432 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 458 through 467 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 335 through 349 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 350 through 362 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 363 through 385 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 386 through 405 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 406 through 423 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 424 through 457 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 458 through 467 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 17 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 17 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 64 through 78 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 84 through 90 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 64 through 78)
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 84 through 90 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 363 through 371)
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 433 through 439)
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 440 through 457)
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 79 through 83)
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 79 through 83)

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Yorodumi