PDB-4fxw: Structure of phosphorylated SF1 complex with U2AF65-UHM domain

ID or keywords:

Entry

Database: PDB / ID: 4fxw

Title

Structure of phosphorylated SF1 complex with U2AF65-UHM domain

Components

Splicing factor 1
Splicing factor U2AF 65 kDa subunit

Keywords

PROTEIN BINDING / UHM / pre-mRNA splicing factor / phosphorylation

Function / homology

Function and homology information

nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Leydig cell differentiation / male sex determination / mRNA 3'-end processing / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.29 Å

Authors

Wang, W. / Bauer, W.J. / Wedekind, J.E. / Kielkopf, C.L.

Citation

Journal: Structure / Year: 2013
Title: Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex.
Authors: Wang, W. / Maucuer, A. / Gupta, A. / Manceau, V. / Thickman, K.R. / Bauer, W.J. / Kennedy, S.D. / Wedekind, J.E. / Green, M.R. / Kielkopf, C.L.

History

Deposition	Jul 3, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fxw.cif.gz	186.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4fxw.ent.gz	160.3 KB	Display	PDB format
PDBx/mmJSON format	4fxw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fxw_validation.pdf.gz	471.6 KB	Display	wwPDB validaton report
Full document	4fxw_full_validation.pdf.gz	479.1 KB	Display
Data in XML	4fxw_validation.xml.gz	18.9 KB	Display
Data in CIF	4fxw_validation.cif.gz	25 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/4fxw ftp://data.pdbj.org/pub/pdb/validation_reports/fx/4fxw	HTTPS FTP

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Related structure data

Related structure data	4fxxC 1k1g 1opi 2g4b C: citing same article (ref.)
Similar structure data	4ftr-d 4ftn-d 4ftq-d 4oda-1 4od8-1 4fto-d 5jks-1 4hyi-d 2ym4-d 2e9p-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	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #86 - Feb 2007 Exosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (1) #65 - May 2005 Self-splicing RNA similarity (1)

Deposited unit

A: Splicing factor U2AF 65 kDa subunit

B: Splicing factor 1

C: Splicing factor U2AF 65 kDa subunit

D: Splicing factor 1

hetero molecules

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

1

A: Splicing factor U2AF 65 kDa subunit

B: Splicing factor 1

hetero molecules

defined by author&software
27.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Splicing factor U2AF 65 kDa subunit

D: Splicing factor 1

hetero molecules

defined by author&software
27 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.800, 116.100, 130.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	D-218- HOH

#1: Protein	Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit Mass: 12236.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P26368
#2: Protein	Splicing factor 1 / Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene ...Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene in MEN1 locus / Zinc finger protein 162 Mass: 14639.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q15637
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.7 Å³/Da / Density % sol: 54.45 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.9219, 0.9794, 0.9793

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2011

Radiation

Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9219	1
2	0.9794	1
3	0.9793	1

Reflection

Resolution: 2.29→50 Å / Num. obs: 50161 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / R_merge(I) obs: 0.062 / Χ²: 1.583 / Net I/σ(I): 28.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.29-2.33	3	0.619	2689	1.392	1	99.7
2.33-2.38	3.1	0.511	2617	0.985	1	99.5
2.38-2.42	3.2	0.381	2639	1.002	1	99.7
2.42-2.48	3.3	0.309	2626	1.024	1	99.5
2.48-2.53	3.3	0.272	2645	1.067	1	100
2.53-2.6	3.4	0.237	2645	1.035	1	100
2.6-2.67	3.4	0.207	2628	1.08	1	100
2.67-2.75	3.4	0.168	2604	1.156	1	99.8
2.75-2.83	3.4	0.12	2677	1.429	1	100
2.83-2.94	3.4	0.104	2648	1.245	1	100
2.94-3.05	5.6	0.135	2650	1.28	1	100
3.05-3.19	5.8	0.118	2656	1.585	1	100
3.19-3.36	5.8	0.094	2649	1.7	1	100
3.36-3.57	5.8	0.078	2642	1.92	1	100
3.57-3.85	5.8	0.071	2642	2.029	1	100
3.85-4.23	5.8	0.067	2646	2.092	1	99.9
4.23-4.85	5.8	0.057	2633	2.347	1	100
4.85-6.1	5.8	0.05	2644	1.668	1	100
6.1-50	5.1	0.039	2555	1.584	1	95.5
				1.539	1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
Web-Ice		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.29→34.56 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.645 / SU ML: 0.39 / σ(F): 0 / Phase error: 39.51 / Stereochemistry target values: LS_WUNIT_K1

	R_factor	Num. reflection	% reflection
R_free	0.2807	3951	8.74 %
R_work	0.2484	-	-
obs	0.2513	45220	89.42 %

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 70.436 Å² / k_sol: 0.282 e/Å³

Displacement parameters

B_iso max: 262.19 Å² / B_iso mean: 105.0561 Å² / B_iso min: 37.01 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	47.6199 Å²	-0 Å²	-0 Å²
2-	-	-27.4242 Å²	-0 Å²
3-	-	-	-20.1957 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→34.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3273	0	15	56	3344

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3429
X-RAY DIFFRACTION	f_angle_d	0.656	4670
X-RAY DIFFRACTION	f_chiral_restr	0.044	502
X-RAY DIFFRACTION	f_plane_restr	0.004	623
X-RAY DIFFRACTION	f_dihedral_angle_d	14.263	1329

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.29-2.3179	0.4604	108	0.4348	1175	1283	68
2.3179-2.3473	0.4977	110	0.4443	1200	1310	74
2.3473-2.3782	0.4161	125	0.4157	1271	1396	77
2.3782-2.4107	0.4054	122	0.4355	1287	1409	78
2.4107-2.4452	0.4168	122	0.4091	1264	1386	78
2.4452-2.4817	0.4042	116	0.3728	1291	1407	78
2.4817-2.5204	0.3689	131	0.4195	1371	1502	84
2.5204-2.5617	0.3713	120	0.367	1360	1480	81
2.5617-2.6059	0.4716	127	0.3775	1356	1483	83
2.6059-2.6533	0.4963	138	0.3863	1395	1533	85
2.6533-2.7043	0.3554	137	0.3612	1379	1516	85
2.7043-2.7594	0.3035	148	0.3613	1432	1580	86
2.7594-2.8194	0.4337	133	0.3578	1489	1622	90
2.8194-2.885	0.3576	136	0.3551	1511	1647	91
2.885-2.9571	0.3429	152	0.3285	1519	1671	92
2.9571-3.037	0.2887	146	0.3251	1557	1703	95
3.037-3.1263	0.3789	152	0.3364	1584	1736	96
3.1263-3.2271	0.4468	159	0.3275	1615	1774	98
3.2271-3.3424	0.3408	152	0.2986	1625	1777	98
3.3424-3.4761	0.3375	156	0.2799	1609	1765	99
3.4761-3.6341	0.2469	160	0.2534	1613	1773	98
3.6341-3.8255	0.3013	156	0.2428	1609	1765	99
3.8255-4.0648	0.2619	162	0.2273	1660	1822	99
4.0648-4.3781	0.2482	161	0.1872	1616	1777	99
4.3781-4.8177	0.1884	160	0.174	1638	1798	100
4.8177-5.5124	0.1882	152	0.1896	1651	1803	100
5.5124-6.9358	0.2445	156	0.2162	1654	1810	100
6.9358-34.5641	0.2517	154	0.1832	1538	1692	94

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	5.7791	-1.336	-4.9495	4.8009	3.2549	5.1732	0.3806	-0.1704	-0.0054	0.7258	0.285	-0.0512	-0.3339	1.5031	0.0356	0.453	0.0611	-0.067	0.3803	-0.0752	0.3665	26.9645	18.4913	70.393
2	1.5286	1.5142	-4.9781	7.2057	-0.8396	2.0003	0.6999	0.6748	0.7253	-1.9819	0.5347	-0.3716	-0.9374	-4.6439	-0.0199	1.5624	0.5064	-0.1564	1.1268	0.1395	1.0528	14.0186	26.0629	58.3606
3	8.0253	-1.2039	-3.5466	2.8869	0.8376	3.9972	-0.4176	0.3981	-0.4327	0.4228	-0.9344	1.3197	1.6438	-1.5721	0.3455	0.8799	-0.1042	-0.0323	0.8069	-0.2452	0.9599	14.4979	13.7176	67.9908
4	5.4017	-1.4996	5.3022	2.0628	1.0899	9.2118	-0.9322	1.4823	1.9312	-0.5606	-0.6375	1.3142	-3.4633	0.0492	0.4864	1.3034	0.5685	-0.2101	0.7933	-0.0115	1.0087	17.7098	30.9282	66.1291
5	1.8161	-1.4102	-2.436	5.9871	2.8075	4.9138	-0.0441	0.0509	-0.4968	0.2102	-0.0617	-0.0581	1.3142	0.8106	0.1673	0.7604	0.2395	-0.1269	0.6958	-0.0838	0.5972	25.315	15.3622	71.2547
6	1.5304	-0.4224	-0.9766	6.8466	4.1014	2.8156	1.694	0.5054	-0.5672	0.5836	-0.5214	0.2158	-1.1908	0.3316	0.1303	0.9766	0.0346	-0.1593	0.6106	-0.1301	0.6923	22.056	27.743	77.7332
7	6.4541	-3.7666	-2.7451	7.3442	7.0792	9.7936	0.0753	1.1711	-1.3424	0.6931	0.7296	-0.5765	1.0013	1.6588	-0.5545	0.9773	0.2302	-0.0608	0.9508	0.0813	0.6089	30.6181	13.8867	62.24
8	6.3921	0.3168	4.7903	6.5222	0.1876	3.8665	0.1758	0.4192	0.404	-0.6618	0.3072	-0.6909	-0.0317	3.1576	-0.675	0.7562	-0.163	0.1626	1.0464	-0.0879	0.706	34.3915	22.8428	57.3961
9	8.8675	-7.0736	4.0404	7.9608	-1.3696	4.8476	0.8708	-2.3148	-2.7096	-0.5092	1.1204	0.8003	2.1978	-0.426	-0.3127	1.4853	-0.0732	-0.0261	0.9231	0.0426	0.9115	16.5611	15.5247	43.6781
10	2.3037	-0.4821	3.789	-0.0841	-0.3822	7.2958	0.2781	-0.2873	0.1284	0.0304	-0.1908	-0.2646	-0.4832	0.7077	-0.0327	1.1388	-0.1245	-0.0553	0.6403	-0.0528	0.4477	23.7829	26.2931	41.2128
11	5.2361	-1.981	-0.1568	6.2204	-1.4704	2.481	0.392	2.4277	2.0564	-0.2281	1.9014	0.318	0.8242	0.572	-1.7811	2.0638	0.3246	0.2451	1.6015	-0.1948	0.6118	42.4941	31.9643	53.2983
12	7.6235	-2.3465	-2.5995	8.7513	7.9816	9.762	0.1568	0.3419	0.2436	-1.9521	-1.7641	0.7902	0.5742	-0.4584	0.7886	0.9236	0.1319	0.0145	0.486	0.0843	0.4594	21.1853	47.4373	80.6612
13	5.1759	-0.8791	-5.1015	2.3832	-0.1229	5.4575	1.5974	0.0441	2.5398	3.2178	0.3931	-0.6229	0.4833	-0.732	-2.6585	1.9853	-0.2193	-0.3107	0.7402	0.1293	1.5068	26.6221	65.0911	82.6551
14	4.4356	-2.8205	0.3205	5.8179	-4.5913	5.3942	-0.4959	-0.3385	0.9677	1.6461	0.715	-1.7346	-1.6212	0.4529	-0.1151	1.1025	-0.1878	-0.3414	0.8851	0.0466	1.0746	32.6675	53.6927	87.8539
15	8.3619	2.2559	-1.9507	4.7416	3.1332	3.7112	0.2587	0.7506	0.6751	-1.0369	-1.0009	-1.0582	-1.7666	1.0234	0.3154	1.1716	-0.0374	0.0544	0.7411	0.1565	0.8907	28.5062	54.2414	77.3896
16	7.6391	-3.1543	1.4183	7.4591	-5.4751	4.188	1.4869	0.6644	-0.8919	-3.0364	-1.981	-0.7097	0.0732	1.1845	0.7463	1.097	0.0637	-0.0138	0.7386	0.2187	0.829	28.1805	45.12	79.9747
17	4.3035	-5.9904	-5.4389	8.5998	7.2535	6.8627	0.0339	0.2091	-0.183	-0.7205	-0.167	1.0729	-0.7315	-0.1524	-0.0323	0.7394	0.1688	0.0298	0.407	0.0802	0.5035	23.3899	38.6076	86.3635
18	9.922	-2.6968	1.9553	4.3155	-5.6607	7.7963	-0.2634	-0.0175	-0.2781	1.0943	-0.1629	0.8133	-1.1351	0.3164	0.4508	0.8008	0.0132	0.0184	0.6045	-0.1009	0.6484	18.9895	53.1593	91.6841
19	6.2164	2.5475	-5.428	4.5417	-1.5169	5.2802	-0.6447	0.9987	-0.0132	-2.7998	-0.5697	-0.0111	0.2496	-0.0706	0.791	1.3215	0.184	-0.0391	0.9119	0.076	0.5872	24.2522	46.1335	72.9576
20	7.3498	-0.3701	-0.7869	7.5629	-1.0372	4.2425	0.5728	0.4411	-0.3286	-0.002	-0.6125	1.5562	0.3342	-0.2855	0.3667	0.9529	0.0841	-0.2917	0.3791	-0.1956	0.8241	12.1034	53.3635	87.0556
21	8.5133	0.8854	-0.2479	7.2717	1.8227	6.5201	-0.7023	-0.3204	-0.9864	-0.2683	0.7127	-0.7005	1.7126	0.455	0.1871	0.9308	0.0009	0.1941	0.3705	-0.0442	0.4032	18.0783	74.0854	103.6968
22	7.0856	-1.0952	2.1608	7.2591	-1.442	8.4579	0.6216	1.1594	-0.4894	-1.3343	-0.7507	2.5199	-0.2518	-0.1485	0.4447	1.0463	0.2229	-0.3623	0.5247	-0.2854	1.4879	7.7406	67.1069	86.717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 371:385)	A	371 - 385
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 386:391)	A	386 - 391
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 392:416)	A	392 - 416
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 417:430)	A	417 - 430
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 431:470)	A	431 - 470
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 471:475)	A	471 - 475
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 20:45)	B	20 - 45
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 46:66)	B	46 - 66
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 67:83)	B	67 - 83
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 84:118)	B	84 - 118
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 119:128)	B	119 - 128
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 371:385)	C	371 - 385
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 386:391)	C	386 - 391
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 392:408)	C	392 - 408
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 409:430)	C	409 - 430
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 431:438)	C	431 - 438
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 439:449)	C	439 - 449
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 450:459)	C	450 - 459
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 460:475)	C	460 - 475
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 19:67)	D	19 - 67
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 68:96)	D	68 - 96
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 97:132)	D	97 - 132

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