PDB-3oak: Crystal structure of a Spn1 (Iws1)-Spt6 complex

ID or keywords:

Entry

Database: PDB / ID: 3oak

Title

Crystal structure of a Spn1 (Iws1)-Spt6 complex

Components

Transcription elongation factor SPT6
Transcription factor IWS1

Keywords

TRANSCRIPTION / Transcription factor complex / Nucleus

Function / homology

Function and homology information

carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / nucleosome organization / regulation of transcription elongation by RNA polymerase II / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / RNA polymerase II complex binding / nucleosome binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.15 Å

Authors

McDonald, S.M. / Close, D. / Hill, C.P.

Citation

Journal: Mol.Cell / Year: 2010
Title: Structure and biological importance of the spn1-spt6 interaction, and its regulatory role in nucleosome binding.
Authors: McDonald, S.M. / Close, D. / Xin, H. / Formosa, T. / Hill, C.P.

History

Deposition	Aug 5, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 16, 2011	Group: Atomic model
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	3oak.cif.gz	228.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3oak.ent.gz	191.1 KB	Display	PDB format
PDBx/mmJSON format	3oak.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3oak_validation.pdf.gz	449.7 KB	Display	wwPDB validaton report
Full document	3oak_full_validation.pdf.gz	455 KB	Display
Data in XML	3oak_validation.xml.gz	18.2 KB	Display
Data in CIF	3oak_validation.cif.gz	26.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/3oak ftp://data.pdbj.org/pub/pdb/validation_reports/oa/3oak	HTTPS FTP

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Related structure data

Related structure data	3o8zC C: citing same article (ref.)
Similar structure data	3v9p-2 3fpu-d 2jbf-4 6op8-d 4jkh-2 4zkc-d 6kc5-d 2wwm-2 2j7v-4 2wwk-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	#55 - Jul 2004 DNA Ligase similarity (1)

Deposited unit

A: Transcription factor IWS1

B: Transcription factor IWS1

C: Transcription elongation factor SPT6

D: Transcription elongation factor SPT6

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

1

A: Transcription factor IWS1

D: Transcription elongation factor SPT6

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

2

B: Transcription factor IWS1

C: Transcription elongation factor SPT6

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

Unit cell

Length a, b, c (Å)	105.858, 68.697, 73.966
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-6- HOH
2	1	B-59- HOH

#1: Protein	Transcription factor IWS1 / Interacts with SPT6 protein 1 / Suppresses postrecruitment functions protein 1 Mass: 17045.719 Da / Num. of mol.: 2 / Fragment: Spn1 core domain, UNP reisudes 148-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: IWS1, SPN1, YPR133C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06505
#2: Protein/peptide	Transcription elongation factor SPT6 / Chromatin elongation factor SPT6 Mass: 3722.953 Da / Num. of mol.: 2 / Fragment: Spt6 N-terminal segment, UNP residues 239-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPT6, CRE2, SSN20, YGR116W, G6169 / Production host: Escherichia coli (E. coli) / References: UniProt: P23615
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.24 Å³/Da / Density % sol: 62.01 %
Crystal grow	Temperature: 293 K / pH: 6.5 Details: 0.2 M magnesium acetate, 0.1 M MES pH 6.5, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2009
Radiation	Monochromator: varimax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.15→30 Å / Num. obs: 30152 / % possible obs: 100 %
Reflection shell	Resolution: 2.15→2.23 Å / R_merge(I) obs: 0.544 / % possible all: 100

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.15 Å	29.87 Å
Translation	2.15 Å	29.87 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	1.3.3	phasing
PHENIX	1.6_289	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→27.73 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Phase error: 22.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.244	1526	5.07 %
R_work	0.186	-	-
obs	0.189	30095	99.8 %
all	-	30152	-

Solvent computation

Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.73 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso mean: 62.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.6397 Å²	0 Å²	0 Å²
2-	-	1.5107 Å²	-0 Å²
3-	-	-	5.1289 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→27.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2903	0	0	268	3171

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2952
X-RAY DIFFRACTION	f_angle_d	1.279	3995
X-RAY DIFFRACTION	f_dihedral_angle_d	16.384	1111
X-RAY DIFFRACTION	f_chiral_restr	0.065	464
X-RAY DIFFRACTION	f_plane_restr	0.005	510

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 (%)
2.15-2.2227	0.2664	160	0.2322	2745	X-RAY DIFFRACTION	99
2.2227-2.3117	0.2722	175	0.208	2800	X-RAY DIFFRACTION	100
2.3117-2.4168	0.2417	138	0.1969	2811	X-RAY DIFFRACTION	100
2.4168-2.5442	0.281	146	0.1853	2847	X-RAY DIFFRACTION	100
2.5442-2.7035	0.2345	140	0.1771	2840	X-RAY DIFFRACTION	100
2.7035-2.912	0.2403	140	0.1801	2843	X-RAY DIFFRACTION	100
2.912-3.2046	0.2599	164	0.1875	2874	X-RAY DIFFRACTION	100
3.2046-3.6675	0.2266	165	0.1735	2857	X-RAY DIFFRACTION	100
3.6675-4.6172	0.2189	147	0.147	2922	X-RAY DIFFRACTION	100
4.6172-27.7375	0.23	151	0.1945	3030	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	0.0322	0.0485	-0.0413	0.0572	-0.0311	0.0031	0.0803	-0.1967	0.2758	1.535	-0.7233	-0.3805	-0.9177	-1.3031	0.0027	0.3902	-0.0425	0.2967	1.1972	-0.5483	1.6518	-38.1764	33.4262	-13.5807
2	0.5243	-0.0475	0.1452	0.2398	0.0527	0.4308	-0.5731	-0.8472	0.397	-0.4071	0.8283	1.4924	0.6193	-1.4929	-0.0003	0.4541	0.0723	-0.0426	0.4844	0.0122	0.5672	-33.9762	40.8771	-13.4106
3	1.0505	0.8345	1.0017	2.0367	1.2724	3.1086	0.2963	0.4525	-0.3263	-0.591	-0.0439	0.2065	-0.1109	-0.2385	-0.0003	0.3022	-0.0291	0.0146	0.306	-0.0619	0.2171	-15.9051	29.4518	-14.5999
4	0.2728	-0.2441	-0.2677	0.1816	0.1784	0.2398	-0.1029	0.0036	0.3443	0.6315	0.3435	-1.5483	-0.0773	0.5486	-0.0013	0.3342	0.157	0.0943	0.478	-0.1227	1.0944	3.2482	22.9337	-16.9753
5	0.6919	0.1468	-0.1151	-0.0479	0.1728	0.4801	0.0365	0.3304	0.1048	-0.4448	-0.1625	0.1618	-0.2687	0.2115	-0.0005	0.3505	-0.0152	-0.013	0.3399	0.0263	0.3379	-13.1064	37.6176	-8.9274
6	0.6288	0.79	0.3116	1.5043	-1.2883	4.1542	0.0849	-0.2861	-0.3188	-0.1096	-0.0826	-0.0547	-0.0251	-0.0134	-0.0002	0.3376	-0.0301	0.003	0.303	0.0178	0.3396	-14.3577	29.7813	-3.819
7	1.8399	0.269	0.3502	1.3364	-1.7493	1.8764	0.186	-0.9153	-0.2861	0.2591	0.0636	0.1581	0.302	-0.4419	0.0002	0.3821	-0.0983	-0.0198	0.4302	0.0964	0.3752	-18.354	25.2681	3.2694
8	0.3547	0.1447	-0.5717	0.4798	-0.374	0.7556	0.5156	-0.9091	-1.111	-0.9171	-0.5742	-1.6978	-0.0583	0.3674	0.0047	0.4613	-0.1974	0.0039	0.5775	0.1722	0.6178	-1.9419	27.0486	5.978
9	0.8752	-0.0774	-0.0945	0.632	-0.1243	0.8772	1.416	0.2165	0.753	-0.4315	-0.7296	-0.9472	-0.6265	1.3068	-0.0044	0.5325	-0.2038	-0.1362	0.4346	-0.0534	0.3962	-12.259	28.5834	11.1321
10	0.098	-0.0176	-0.0901	0.6923	-0.3487	0.2165	-0.5403	-0.0916	1.0941	1.4905	0.1538	0.3389	-1.0201	-0.7327	0.0011	0.4258	-0.2657	0.0007	0.9567	-0.0716	0.6581	-21.9077	26.354	12.7663
11	0.1543	-0.0972	-0.131	0.0425	0.0724	0.1093	-1.2566	-0.474	-0.3171	-1.9922	-0.4101	-1.3605	-1.6091	0.995	-0.0022	0.62	0.0329	0.1462	1.2715	0.1756	0.6911	-15.5117	39.8177	-20.7896
12	0.5599	1.1184	0.6838	1.7714	-0.6964	1.7362	0.5205	-0.5094	-0.5004	0.927	-0.5039	-1.21	-0.0408	0.4196	0.0017	0.3411	0.0023	-0.0174	0.3482	0.0314	0.3438	-31.9872	36.0769	-23.0003
13	0.0491	-0.014	0.0195	0.1171	0.0385	0.0371	1.0431	-0.2435	0.1991	1.6066	0.1288	1.1129	1.9937	-0.2854	-0.0001	1.2971	-0.3515	-0.1047	1.4323	0.2325	0.5482	-50.7754	18.5862	-21.6998
14	0.3788	0.2205	0.8678	0.1492	0.221	4.8993	0.667	-1.0257	-0.5071	0.3014	-0.2633	1.1798	-0.2178	-1.5437	-0.0664	0.6247	-0.5676	0.1247	1.1641	0.3484	1.1587	-55.074	20.1385	-19.5573
15	0.4451	-0.3335	0.0734	0.764	-0.2841	0.1125	0.0257	-0.3289	0.5056	0.6225	0.1032	0.9134	-0.5358	-1.4465	0.012	0.3851	0.0386	0.02	0.5829	0.0183	0.4542	-45.2191	35.7008	-24.9759
16	1.3648	0.2076	0.6038	2.3097	1.5219	3.9656	-0.1744	-0.0587	-0.1328	-0.1442	-0.0694	-0.111	0.0535	0.2316	-0	0.3526	0.0293	0.0106	0.3097	0.0042	0.3216	-35.544	33.6175	-32.3801
17	0.6268	-0.2685	0.7259	1.085	-0.287	0.7723	0.0168	0.1397	0.4492	-0.3688	-0.05	0.0722	-0.1722	-0.2941	-0.0001	0.4026	0.0105	0.0031	0.3821	-0.0178	0.3765	-40.8485	36.3578	-38.8731
18	0.8269	-0.2305	-0.8464	1.4095	1.2569	1.7406	0.254	0.3791	-1.0317	-0.0783	0.0605	-0.5009	0.3846	0.2809	-0.0005	0.4118	0.0359	0.0108	0.5054	-0.0939	0.34	-34.1385	26.0672	-40.96
19	0.7084	-0.6988	-0.0435	0.7558	0.2635	0.4947	0.3003	0.5254	-0.395	0.1656	-0.2595	0.8079	-1.3566	-1.4125	0.0008	0.4895	0.1182	-0.0589	0.557	-0.0368	0.3882	-46.2507	30.1514	-45.9459
20	0.1667	0.0755	-0.0581	0.1183	0.1676	0.1862	-0.7758	2.1427	-0.2901	-0.7539	0.036	0.2975	0.03	-0.4761	-0.0015	0.4407	-0.0125	0.0124	0.5695	-0.0576	0.3448	-31.7474	31.2646	-49.6263
21	1.3791	-0.5994	-0.7352	0.3135	-0.1196	1.1178	0.2416	-0.5894	1.3948	-0.3606	-0.0154	0.0296	-0.6488	1.2833	0.0262	0.5372	0.1216	-0.0418	0.3879	0.0312	0.3929	-19.1897	17.8472	-56.0241
22	0.2845	0.037	0.0398	0.0813	-0.049	0.1111	-0.6541	-0.7044	-0.567	0.0507	-0.2131	-1.3981	0.3687	0.0821	0.0055	0.5848	0.0604	0.0046	0.4046	0.0492	0.5469	-24.7117	19.6034	-46.4018
23	0.2366	-0.2568	0.019	0.2517	0.0162	0.3032	0.4225	0.7138	-1.7347	-1.4401	-0.7696	0.0892	-0.0999	-0.7636	0.0006	0.5779	0.1144	-0.0151	0.4689	-0.247	0.4849	-32.3871	18.9465	-44.0934
24	0.1435	-0.0988	0.0134	0.1846	0.1552	0.1935	0.3718	1.0058	-0.237	0.4254	0.1076	0.2558	0.1743	-0.3384	0	0.5077	-0.0088	-0.12	0.5537	-0.0861	0.618	-41.2543	16.2065	-38.0014
25	1.1339	-0.2148	-0.5559	0.0495	0.1223	0.272	1.4337	2.4989	-0.544	0.0883	-1.3086	-1.025	1.5709	0.8437	-0.0019	1.0284	-0.0056	-0.0887	0.4354	-0.001	0.7227	-49.3168	14.1753	-39.2156
26	0.1015	-0.0489	-0.0134	0.1023	-0.1069	0.2712	-0.3369	0.8756	-0.0509	0.8447	-0.0069	-1.0718	0.9148	-1.6375	-0.0023	0.3635	0.2352	-0.1803	0.9073	-0.1264	1.2463	-33.3596	18.0356	19.6436
27	0.2177	-0.2275	0.0431	0.1705	0.0272	0.311	0.5611	-0.2411	-0.0298	0.6133	-0.7844	0.9388	0.8448	0.0194	0.0002	0.6615	-0.2383	0.0743	0.3378	-0.0113	0.3582	-26.2153	15.5387	11.1407
28	2.0132	-9.0335	-3.9194	5.5807	2.4667	1.3097	-0.4516	0.2982	-2.9385	0.9889	-0.4878	1.5608	0.7493	-1.174	-0.1418	0.4747	-0.08	-0.0028	0.4128	0.1127	0.4323	-18.4565	14.3437	5.3155
29	0.0947	0.0548	0.0375	0.2318	0.0002	0.0186	0.339	0.1414	-0.5176	-0.4911	-0.6442	0.7805	0.138	0.2658	0.0015	0.485	0.0183	-0.0291	0.4286	0.0898	0.7582	-7.7574	14.1189	-0.4591
30	0.1387	-0.0546	0.1013	0.4884	-0.2434	0.1576	1.9256	-0.7637	-0.2538	0.9094	-0.2449	0.3652	0.7283	0.0727	0.0059	0.9761	0.0444	-0.3066	0.3705	0.2054	1.4075	0.5124	13.6957	1.0877

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 resid 142:147)	A	142 - 147
2	X-RAY DIFFRACTION	2	(chain A and resid 148:153)	A	148 - 153
3	X-RAY DIFFRACTION	3	(chain A and resid 154:177)	A	154 - 177
4	X-RAY DIFFRACTION	4	(chain A and resid 178:190)	A	178 - 190
5	X-RAY DIFFRACTION	5	(chain A and resid 191:205)	A	191 - 205
6	X-RAY DIFFRACTION	6	(chain A and resid 206:245)	A	206 - 245
7	X-RAY DIFFRACTION	7	(chain A and resid 246:271)	A	246 - 271
8	X-RAY DIFFRACTION	8	(chain A and resid 272:279)	A	272 - 279
9	X-RAY DIFFRACTION	9	(chain A and resid 280:287)	A	280 - 287
10	X-RAY DIFFRACTION	10	(chain A and resid 288:292)	A	288 - 292
11	X-RAY DIFFRACTION	11	(chain B and resid 142:147)	B	142 - 147
12	X-RAY DIFFRACTION	12	(chain B and resid 148:175)	B	148 - 175
13	X-RAY DIFFRACTION	13	(chain B and resid 176:180)	B	176 - 180
14	X-RAY DIFFRACTION	14	(chain B and resid 181:188)	B	181 - 188
15	X-RAY DIFFRACTION	15	(chain B and resid 189:198)	B	189 - 198
16	X-RAY DIFFRACTION	16	(chain B and resid 199:234)	B	199 - 234
17	X-RAY DIFFRACTION	17	(chain B and resid 235:251)	B	235 - 251
18	X-RAY DIFFRACTION	18	(chain B and resid 252:272)	B	252 - 272
19	X-RAY DIFFRACTION	19	(chain B and resid 273:284)	B	273 - 284
20	X-RAY DIFFRACTION	20	(chain B and resid 285:292)	B	285 - 292
21	X-RAY DIFFRACTION	21	(chain C and resid 233:242)	C	233 - 242
22	X-RAY DIFFRACTION	22	(chain C and resid 243:247)	C	243 - 247
23	X-RAY DIFFRACTION	23	(chain C and resid 248:253)	C	248 - 253
24	X-RAY DIFFRACTION	24	(chain C and resid 254:259)	C	254 - 259
25	X-RAY DIFFRACTION	25	(chain C and resid 260:265)	C	260 - 265
26	X-RAY DIFFRACTION	26	(chain D and resid 235:239)	D	235 - 239
27	X-RAY DIFFRACTION	27	(chain D and resid 240:246)	D	240 - 246
28	X-RAY DIFFRACTION	28	(chain D and resid 247:253)	D	247 - 253
29	X-RAY DIFFRACTION	29	(chain D and resid 254:259)	D	254 - 259
30	X-RAY DIFFRACTION	30	(chain D and resid 260:265)	D	260 - 265

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi