PDB-4f92: Brr2 Helicase Region S1087L

ID or keywords:

Entry

Database: PDB / ID: 4f92

Title

Brr2 Helicase Region S1087L

Components

U5 small nuclear ribonucleoprotein 200 kDa helicase

Keywords

HYDROLASE / RNP remodeling / pre-mRNA splicing / spliceosome catalytic activation / DEXD/H-box RNA Helicase / RNA and ATP binding / Nucleus

Function / homology

Function and homology information

cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.662 Å

Authors

Santos, K.F. / Jovin, S.M. / Weber, G. / Pena, V. / Luehrmann, R. / Wahl, M.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for functional cooperation between tandem helicase cassettes in Brr2-mediated remodeling of the spliceosome.
Authors: Santos, K.F. / Jovin, S.M. / Weber, G. / Pena, V. / Luhrmann, R. / Wahl, M.C.

History

Deposition	May 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 24, 2012	Group: Database references
Revision 1.2	Nov 7, 2012	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4f92.cif.gz	717.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/4f92 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/4f92	HTTPS FTP

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Related structure data

Related structure data	4f91C 4f93C C: citing same article (ref.)
Similar structure data	4f93-d 6s8o-d 4f91-d 5urk-d 5urm-1 5urj-d 4a5a-1 5urm-2 1ekm-d 22773 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	#130 - Oct 2010 Riboswitches similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

B: U5 small nuclear ribonucleoprotein 200 kDa helicase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	146.148, 149.541, 141.324
Angle α, β, γ (deg.)	90.00, 120.33, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD Mass: 197264.312 Da / Num. of mol.: 1 / Fragment: Brr2 Helicase Region / Mutation: S1087L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP200, ASCC3L1, HELIC2, KIAA0788 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75643, RNA helicase
#2: Chemical	ChemComp-SAN / SULFANILAMIDE Mass: 172.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈N₂O₂S / Comment: antibiotic*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.38 Å³/Da / Density % sol: 63.59 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M sodium citrate, 1.2 M sodium Malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 17, 2010
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2.65→50 Å / Num. all: 74938 / Num. obs: 74339 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.65→2.7 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.1 / R_sym value: 0.54 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.662→35.32 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 32.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2592	3746	5.04 %
R_work	0.2117	-	-
obs	0.2142	74339	99.2 %
all	-	74938	-

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 58.507 Å² / k_sol: 0.319 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-11.034 Å²	0 Å²	6.3808 Å²
2-	-	30.8438 Å²	0 Å²
3-	-	-	-19.8098 Å²

Refinement step

Cycle: LAST / Resolution: 2.662→35.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13856	0	11	131	13998

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	14184
X-RAY DIFFRACTION	f_angle_d	0.987	19223
X-RAY DIFFRACTION	f_dihedral_angle_d	18.164	5346
X-RAY DIFFRACTION	f_chiral_restr	0.072	2180
X-RAY DIFFRACTION	f_plane_restr	0.004	2458

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 (%)
2.662-2.6959	0.4047	140	0.3754	2275	X-RAY DIFFRACTION	88
2.6959-2.7314	0.375	154	0.3596	2563	X-RAY DIFFRACTION	100
2.7314-2.7688	0.388	136	0.3358	2651	X-RAY DIFFRACTION	100
2.7688-2.8083	0.3575	145	0.3308	2624	X-RAY DIFFRACTION	100
2.8083-2.8502	0.3892	130	0.3243	2584	X-RAY DIFFRACTION	100
2.8502-2.8947	0.3182	121	0.3023	2661	X-RAY DIFFRACTION	100
2.8947-2.9422	0.3445	121	0.2924	2636	X-RAY DIFFRACTION	100
2.9422-2.9929	0.3398	136	0.2769	2637	X-RAY DIFFRACTION	100
2.9929-3.0473	0.3467	129	0.2889	2628	X-RAY DIFFRACTION	100
3.0473-3.1058	0.3179	151	0.2723	2588	X-RAY DIFFRACTION	100
3.1058-3.1692	0.3661	149	0.2659	2647	X-RAY DIFFRACTION	100
3.1692-3.2381	0.342	114	0.2612	2627	X-RAY DIFFRACTION	100
3.2381-3.3133	0.3321	143	0.2508	2616	X-RAY DIFFRACTION	100
3.3133-3.3961	0.318	117	0.2345	2668	X-RAY DIFFRACTION	100
3.3961-3.4879	0.2796	127	0.2209	2670	X-RAY DIFFRACTION	100
3.4879-3.5904	0.3243	124	0.2174	2616	X-RAY DIFFRACTION	100
3.5904-3.7062	0.2544	158	0.2091	2566	X-RAY DIFFRACTION	100
3.7062-3.8385	0.2632	154	0.2051	2630	X-RAY DIFFRACTION	100
3.8385-3.992	0.2549	122	0.1906	2643	X-RAY DIFFRACTION	99
3.992-4.1734	0.2159	158	0.1742	2601	X-RAY DIFFRACTION	100
4.1734-4.393	0.2202	158	0.1597	2628	X-RAY DIFFRACTION	100
4.393-4.6677	0.2049	143	0.1579	2622	X-RAY DIFFRACTION	100
4.6677-5.0271	0.1995	129	0.1575	2657	X-RAY DIFFRACTION	100
5.0271-5.5313	0.2325	151	0.1823	2633	X-RAY DIFFRACTION	100
5.5313-6.3277	0.2357	138	0.2212	2628	X-RAY DIFFRACTION	100
6.3277-7.9572	0.2675	134	0.1787	2683	X-RAY DIFFRACTION	99
7.9572-35.3231	0.1921	164	0.1808	2611	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	1.2529	0.4099	-0.4826	1.1488	-0.3222	0.9315	0.3026	-0.0314	0.397	0.2997	-0.3919	-0.3941	-0.4258	0.8994	0.0036	0.7224	-0.3054	-0.1726	0.9648	0.1424	0.6964	-5.6582	15.7953	-40.0361
2	1.9006	-0.1475	-0.2146	2.885	-0.6447	3.3303	0.152	-0.2303	0.5312	0.3127	-0.2002	0.3114	-0.5601	0.4444	-0.0117	0.4917	-0.2509	-0.0258	0.2659	-0.0211	0.6301	-24.954	13.6995	-37.8096
3	1.7882	0.1638	-0.2269	1.0766	-0.7127	0.9998	0.0061	-0.6011	0.4229	0.6278	-0.1019	-0.2375	-0.7363	0.5905	0.0252	0.7021	-0.6985	-0.414	1.1822	0.1543	0.7767	-0.8882	19.7774	-18.352
4	1.3168	-0.4495	0.6041	2.1684	0.0963	2.358	-0.0898	0.3463	-0.1625	-0.0012	-0.1392	-0.2085	0.4067	0.759	-0.0038	0.3883	0.0574	-0.0454	0.5142	0.0608	0.436	-20.0926	-11.6191	-41.4625
5	3.1591	-0.9938	-0.465	1.3699	0.0797	2.4095	-0.0541	-0.5273	0.0147	0.2935	0.0074	-0.2442	0.2654	0.6505	-0.0024	0.4978	0.0572	-0.1088	0.478	0.0957	0.3704	-20.8038	-9.6279	-9.7936
6	0.6698	-0.0149	0.2124	0.8795	0.4456	0.321	-0.0041	-0.8726	0.561	0.58	0.1388	-0.0525	-0.0473	0.6819	0.0002	0.8534	-0.0897	0.0296	0.9194	-0.2375	0.6403	-38.4773	7.2387	7.9636
7	3.548	1.8582	0.2556	0.9917	0.3735	3.1988	-0.0048	-0.4057	-0.0759	0.1805	-0.28	0.1416	0.3212	-0.3225	-0.025	0.4516	-0.0779	0.0396	0.2626	-0.0349	0.3957	-51.5142	-9.5008	-11.056
8	1.9126	-0.8154	-1.1984	2.3685	0.3733	2.8573	-0.1211	0.8524	-0.2436	-0.2847	-0.0846	0.2449	0.371	-1.0957	-0.0656	0.6371	-0.5806	0.0956	0.7786	-0.1699	0.4327	-79.6125	-22.0655	-42.058
9	2.3288	0.1563	-0.5954	0.7911	-0.229	4.5187	-0.0898	0.1955	-0.087	-0.0535	-0.0741	0.0376	0.121	-0.5681	-0.0223	0.3706	-0.165	-0.0147	0.3059	-0.0746	0.4343	-53.0719	-8.3112	-44.0746
10	1.4597	-0.7584	-0.0761	1.7152	0.8905	0.6231	-0.3298	-0.0789	-0.0752	0.2631	0.3373	0.1762	0.0081	-0.345	-0.0096	0.6287	-0.2681	0.193	0.7754	0.0262	0.6273	-85.3553	-12.5927	-16.2202
11	2.1761	-0.4424	0.3838	2.4767	-1.1117	1.9158	0.1593	0.375	0.4474	-0.1146	0.0563	-0.0866	-0.0139	0.059	-0	0.5601	-0.0704	0.0545	0.5524	0.0678	0.62	-77.0823	14.4299	-29.5583
12	0.1108	-0.0904	0.1227	0.1536	-0.0238	0.207	0.1258	0.9366	0.1887	-0.5838	0.3495	0.13	-0.6084	0.0696	-0.0004	1.1807	0.1514	0.1094	1.7974	0.3038	0.834	-84.2073	27.2567	-55.4472
13	1.3757	0.3316	0.4026	1.6854	-1.2631	1.2756	0.3393	0.9372	0.0377	-0.2114	0.0521	0.5089	0.2397	-0.5512	0.0093	0.5832	-0.0012	-0.0571	1.5077	0.2198	0.8897	-102.8074	17.2349	-37.0903

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN B AND RESSEQ 403:486)
2	X-RAY DIFFRACTION	2	(CHAIN B AND RESSEQ 487:683)
3	X-RAY DIFFRACTION	3	(CHAIN B AND RESSEQ 684:888)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESSEQ 889:993)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESSEQ 994:1125)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESSEQ 1126:1181)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESSEQ 1182:1294)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESSEQ 1295:1521)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESSEQ 1522:1724)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESSEQ 1725:1824)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESSEQ 1825:1957)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESSEQ 1958:2014)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESSEQ 2015:2125)

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