PDB-4ilh: Crystal structure of an Aar2p C-terminal deletion mutant in conpl...

ID or keywords:

Entry

Database: PDB / ID: 4ilh

Title

Crystal structure of an Aar2p C-terminal deletion mutant in conplex with Prp8p RNaseH

Components

A1 cistron-splicing factor AAR2
Pre-mRNA-splicing factor 8

Keywords

SPLICING / U5 snRNP assembly / Aar2 / Prp8

Function / homology

Function and homology information

generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Weber, G. / Heroven, A.C. / Santos, K.F. / Wahl, M.C.

Citation

Journal: To be Published
Title: Structural basis for the Aar2p-mediated regulation of Prp8p interactions with Brr2p and U4/U6 di-snRNA
Authors: Weber, G. / Cristao, V. / Santos, K.F. / Mozzafari Jovin, S. / Heroven, A.C. / Luehrmann, R. / Beggs, J.D. / Wahl, M.C.

History

Deposition	Dec 31, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	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	4ilh.cif.gz	250.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ilh.ent.gz	199.5 KB	Display	PDB format
PDBx/mmJSON format	4ilh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ilh_validation.pdf.gz	438.6 KB	Display	wwPDB validaton report
Full document	4ilh_full_validation.pdf.gz	443.8 KB	Display
Data in XML	4ilh_validation.xml.gz	26.4 KB	Display
Data in CIF	4ilh_validation.cif.gz	40 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/il/4ilh ftp://data.pdbj.org/pub/pdb/validation_reports/il/4ilh	HTTPS FTP

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Related structure data

Related structure data	3sbtS 4ilg 4ili 4ilj S: Starting model for refinement
Similar structure data	5qzb-d 5qyn-d 5r0d-d 5qzw-d 5r1b-d 3sbt-1 5qyq-d 5qzg-d 5qyl-d 5qys-d 5r0g-d 5qym-d 5qzh-d 5r1n-d 5qzp-d 5r1e-d 5r0w-d 5r0y-d 5qyx-d 5qyw-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
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (22) #166 - Oct 2013 Proteasome similarity (4)

Deposited unit

A: Pre-mRNA-splicing factor 8

B: A1 cistron-splicing factor AAR2

69.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	79.890, 76.760, 91.860
Angle α, β, γ (deg.)	90.00, 105.88, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-2345- HOH

#1: Protein	Pre-mRNA-splicing factor 8 Mass: 29501.113 Da / Num. of mol.: 1 / Fragment: yPrp8 RNaseH (UNP Residues 1835-2096) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#2: Protein	A1 cistron-splicing factor AAR2 Mass: 39957.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 513 / 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: 1.95 Å³/Da / Density % sol: 36.93 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl, pH 8.0, 19 % (w/v) PEG 4000 and 100 mM KCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 17, 2012
Radiation	Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.85→35 Å / Num. all: 45624 / Num. obs: 45500 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / R_merge(I) obs: 0.08 / R_sym value: 0.07 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.85→1.9 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / R_sym value: 0.74 / % possible all: 100

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SBT

3sbt

Resolution: 1.85→33.953 Å / SU ML: 0.24 / Phase error: 23.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2174	2275	5 %	RANDOM
R_work	0.1679	-	-	-
all	0.1703	45624	-	-
obs	0.1703	45497	99.8 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.53 Å² / k_sol: 0.349 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	13.4365 Å²	0 Å²	-7.0709 Å²
2-	-	6.4617 Å²	-0 Å²
3-	-	-	8.8554 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→33.953 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4515	0	0	513	5028

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4749
X-RAY DIFFRACTION	f_angle_d	1.157	6448
X-RAY DIFFRACTION	f_dihedral_angle_d	15.056	1783
X-RAY DIFFRACTION	f_chiral_restr	0.08	705
X-RAY DIFFRACTION	f_plane_restr	0.005	829

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 (%)
1.85-1.8902	0.3516	139	0.263	2645	X-RAY DIFFRACTION	100
1.8902-1.9342	0.2841	142	0.241	2695	X-RAY DIFFRACTION	100
1.9342-1.9826	0.2771	141	0.2188	2691	X-RAY DIFFRACTION	100
1.9826-2.0362	0.2928	143	0.2045	2722	X-RAY DIFFRACTION	100
2.0362-2.0961	0.2856	140	0.1961	2649	X-RAY DIFFRACTION	100
2.0961-2.1637	0.2397	141	0.1875	2690	X-RAY DIFFRACTION	100
2.1637-2.241	0.2436	143	0.1805	2706	X-RAY DIFFRACTION	100
2.241-2.3308	0.2492	142	0.175	2705	X-RAY DIFFRACTION	100
2.3308-2.4368	0.2398	143	0.1717	2703	X-RAY DIFFRACTION	100
2.4368-2.5652	0.2137	141	0.1697	2690	X-RAY DIFFRACTION	100
2.5652-2.7259	0.2353	142	0.1822	2703	X-RAY DIFFRACTION	100
2.7259-2.9363	0.239	144	0.1708	2729	X-RAY DIFFRACTION	100
2.9363-3.2315	0.1841	142	0.1623	2706	X-RAY DIFFRACTION	100
3.2315-3.6987	0.1653	143	0.1432	2717	X-RAY DIFFRACTION	100
3.6987-4.658	0.1809	143	0.1295	2710	X-RAY DIFFRACTION	100
4.658-33.9582	0.1885	146	0.1544	2761	X-RAY DIFFRACTION	99

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	0.5484	0.0149	0.1036	1.0848	-0.2235	0.7261	0.0186	0.0162	0.1552	0.0023	-0.0373	-0.0615	-0.1048	-0.0999	-0.0057	0.0298	-0.0178	-0.0342	0.0673	0.0262	0.0724	-5.6273	14.2229	24.5385
2	0.6387	0.4299	0.0353	1.0314	-0.3195	0.7295	-0.0393	-0.0273	-0.2196	-0.0803	0.0457	-0.148	0.1678	0.0631	0.2301	0.0534	-0.0437	-0.0031	0.0144	0.0369	0.0547	2.3221	-4.9558	26.1575
3	0.1479	-0.0293	-0.0577	1.0195	0.0441	0.1033	-0.0261	0.0192	-0.0369	-0.0385	0.0086	0.0135	0.0465	-0.0077	-0.0124	0.0312	-0.0465	0.0085	0.0146	0.0444	0.0116	-9.0506	1.9526	29.4179
4	0.3433	-0.2183	-0.1519	0.6766	0.0367	0.2456	-0.0384	-0.0248	-0.0564	0.053	-0.0055	0.0376	0.039	-0.0015	-0.097	0.0572	-0.079	-0.0106	0.0681	0.0538	0.0253	-13.5418	1.6646	23.0229
5	0.2081	0.1538	-0.0072	0.5507	-0.1895	0.6142	0.0387	0.0269	0.0366	0.0795	0.0225	0.0867	-0.0623	-0.1096	-0.0901	0.0513	-0.0208	0.0017	0.0677	0.0836	0.0432	-15.816	11.1513	21.1923
6	0.226	0.0751	0.0891	0.3105	0.0365	0.4134	0.0504	0.036	-0.0126	0.0374	0.0418	0.0369	0.1049	-0.0954	0.1082	0.0452	-0.0542	0.0001	0.0712	0.0394	0.057	-7.6376	12.1719	31.8059
7	0.3893	-0.0171	-0.0055	0.3818	0.15	0.3869	0.01	-0.0053	-0.0265	0.033	0.0391	-0.047	0.055	0.0477	0.1513	0.0045	0.0551	0.0022	-0.0162	0.0212	0.0224	4.5233	19.5016	34.0127
8	0.8452	-0.0858	0.3729	0.1751	0.1534	0.3851	-0.0132	-0.1406	-0.0709	0.1322	0.0186	0.001	0.145	-0.0016	-0.0414	0.1132	0.0432	-0.0016	0.0419	0.0091	0.0171	2.4048	18.5059	47.5427
9	1.8934	-0.0224	-0.9894	0.9097	-0.5029	1.9149	0.0472	0.1156	0.0668	-0.092	-0.0607	-0.0572	-0.0202	0.0174	-0.0156	0.0279	0.0368	0.0305	0.0136	0.0223	0.0795	10.1132	25.7871	32.7881
10	1.6198	0.7846	-0.1274	1.9417	0.0599	0.8035	-0.0634	0.132	0.1042	-0.0823	0.0113	0.0469	-0.089	0.0497	0.0112	0.1254	-0.0156	-0.0317	0.2136	0.0493	0.1775	8.0904	28.3389	22.0866
11	0.904	-0.1248	0.1016	0.4569	-0.3578	0.512	-0.0033	-0.0104	-0.0764	-0.0425	0.0251	0.0143	0.0478	-0.0163	0.1282	0.003	-0.0151	0.0171	-0.0034	0.008	0.0317	-28.9016	12.5926	-33.4995
12	0.4355	-0.0943	0.0222	0.2024	-0.0555	0.2856	0.0181	-0.0635	-0.0469	-0.0192	0.0465	-0.0053	0.0246	-0.0427	0.1722	-0.014	0.0065	0.0039	0.0198	0.0105	0.0379	-32.3293	12.3099	-29.0435
13	0.7713	0.4524	0.352	0.5139	0.411	0.9585	0.0671	0.0453	-0.1891	-0.0472	-0.0311	0.1364	0.1093	-0.165	0.0145	0.0241	-0.0077	-0.0478	0.0733	0.0178	0.1523	-42.6798	7.665	-34.0508
14	0.459	-0.4785	0.7831	0.7387	-1.3569	2.6402	0.1045	0.085	-0.0411	-0.1228	-0.1104	-0.0439	0.175	0.1246	0.0543	0.066	0.0205	0.0009	0.0257	-0.0195	0.0533	-26.4267	1.6928	-33.1954
15	0.758	-0.0057	0.5455	0.7394	-0.436	0.7605	0.0355	-0.1325	-0.0057	0.0854	0.0305	0.1231	-0.0029	-0.1659	-0.0677	0.0627	-0.0418	0.0333	0.1547	0.0601	0.1014	-37.7065	4.3776	-15.4748
16	0.2604	-0.2226	0.4903	0.6008	-0.8848	1.4531	-0.0738	-0.2136	0.09	0.2527	0.0528	-0.0398	-0.3108	-0.1916	0.0561	0.1281	0.0625	0.0061	0.1305	-0.0074	0.0382	-28.394	11.4265	-5.891
17	0.2211	0.0708	0.1823	0.2809	0.1025	0.8467	0.1263	-0.0539	-0.1012	0.0418	0.014	-0.0636	0.2102	-0.0077	0.6032	0.0665	-0.0168	-0.1234	0.0419	0.0066	-0.1292	-20.6843	-1.8131	-4.8271
18	1.2899	0.1913	0.0032	1.0823	0.0087	1.5167	0.0934	0.0427	0.1465	-0.0842	0.0523	-0.1164	-0.1196	0.1458	0.0473	0.1382	-0.0176	0.0036	0.2011	-0.0216	0.1458	-9.1446	3.5007	-8.8488
19	3.5577	1.8536	-0.1079	2.9938	-0.3275	2.3567	0.0455	-0.1418	-0.0113	0.1578	0.006	-0.1531	0.0133	0.0743	0.018	0.0829	0.0521	-0.0286	0.2005	-0.0697	0.1422	-3.7647	1.177	-14.9891

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1833:1864)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 1865:1882)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 1883:1904)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 1905:1923)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 1924:1947)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 1948:2000)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 2001:2026)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 2027:2044)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 2045:2067)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 2068:2087)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 1:24)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 25:76)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 77:94)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 95:122)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 123:137)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 138:185)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 186:274)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 275:302)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 303:317)

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