PDB-3oci: Crystal structure of TBP (TATA box binding protein)

ID or keywords:

Entry

Database: PDB / ID: 3oci

Title

Crystal structure of TBP (TATA box binding protein)

Components

TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)

Keywords

TRANSCRIPTION / Transcription Initiation

Function / homology

Function and homology information

RNA polymerase II general transcription initiation factor activity / DNA-templated transcription initiation / DNA binding / identical protein binding / nucleus
Similarity search - Function

Biological species

Encephalitozoon cuniculi (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.899 Å

Authors

Cui, S. / Wollmann, P. / Moldt, M. / Hopfner, K.-P.

Citation

Journal: Nature / Year: 2011
Title: Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.
Authors: Wollmann, P. / Cui, S. / Viswanathan, R. / Berninghausen, O. / Wells, M.N. / Moldt, M. / Witte, G. / Butryn, A. / Wendler, P. / Beckmann, R. / Auble, D.T. / Hopfner, K.P.

History

Deposition	Aug 10, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 13, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 20, 2011	Group: Database references / Structure summary
Revision 1.2	Jul 27, 2011	Group: Database references
Revision 1.3	Jan 14, 2015	Group: Other / Structure summary
Revision 1.4	Mar 20, 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	3oci.cif.gz	172.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3oci.ent.gz	137.5 KB	Display	PDB format
PDBx/mmJSON format	3oci.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3oci_validation.pdf.gz	453.6 KB	Display	wwPDB validaton report
Full document	3oci_full_validation.pdf.gz	458.5 KB	Display
Data in XML	3oci_validation.xml.gz	19.6 KB	Display
Data in CIF	3oci_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/3oci ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3oci	HTTPS FTP

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Related structure data

Related structure data	3oc3C C: citing same article (ref.)
Similar structure data	3eik-d 1tbp-d 2z8u-2 1pcz-d 2gd5-2 5l4t-d 2gd5-1 383 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	#67 - Jul 2005 TATA-Binding Protein similarity (6) #88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)

B: TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1)

hetero molecules

49.4 kDa, 2 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)	104.400, 104.400, 129.060
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 20:197 )
2	1	1	chain B and (resseq 20:197 )

#1: Protein	TRANSCRIPTION INITIATION FACTOR TFIID (TFIID-1) / TATA box binding protein Mass: 24502.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU04_1440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ST28
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.76 Å³/Da / Density % sol: 55.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES,2M NaCl,4% Acetone, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2008
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.899→30 Å / Num. all: 41388 / Num. obs: 37329 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.899→2 Å / % possible all: 84.8

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Processing

Software

Name	Version	Classification
remdaq.pilatus		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.899→24.683 Å / SU ML: 0.26 / σ(F): 1.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.215	1950	5.01 %	RANDOM
R_work	0.179	-	-	-
all	0.1965	38913	-	-
obs	0.1826	36954	94.03 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.722 Å² / k_sol: 0.363 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.899→24.683 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2842	0	24	305	3171

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3125
X-RAY DIFFRACTION	f_angle_d	1.08	4235
X-RAY DIFFRACTION	f_dihedral_angle_d	11.369	1202
X-RAY DIFFRACTION	f_chiral_restr	0.072	477
X-RAY DIFFRACTION	f_plane_restr	0.004	544

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1354	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1354	X-RAY DIFFRACTION	POSITIONAL	0.037

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.8987-1.9462	0.277	128	0.2362	2626	93
1.9462-1.9988	0.2569	143	0.2127	2697	97
1.9988-2.0576	0.2008	152	0.1897	2703	96
2.0576-2.124	0.214	142	0.1854	2650	94
2.124-2.1998	0.2285	126	0.189	2637	95
2.1998-2.2879	0.2554	173	0.1927	2683	96
2.2879-2.3919	0.242	137	0.1943	2707	96
2.3919-2.5179	0.2188	147	0.192	2634	95
2.5179-2.6755	0.1914	153	0.1768	2603	93
2.6755-2.8818	0.2155	138	0.1811	2659	95
2.8818-3.1712	0.2207	138	0.1816	2637	93
3.1712-3.6289	0.1657	123	0.1643	2579	92
3.6289-4.5672	0.1739	129	0.149	2608	92
4.5672-24.6854	0.1541	121	0.1645	2535	90

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	0.8892	0.8106	-0.7224	0.9899	-0.6913	0.3063	0.2851	0.2848	0.0665	-0.1347	-0.3492	0.5064	0.027	-0.2004	-0.0012	0.1679	0.0685	0.0031	0.1969	-0.0049	0.23	20.0637	10.0743	-30.6048
2	0.5901	0.3501	-0.6368	0.275	-0.359	0.6666	0.0168	0.0048	0.0281	0.1133	-0.0187	-0.1354	-0.0821	-0.1077	-0	0.2141	0.0275	0.0307	0.1962	-0.0055	0.2059	3.1135	8.6631	-19.1933
3	0.5306	0.5488	-0.5856	0.472	-0.496	0.4503	0.3653	0.3179	0.5016	-0.0342	-0.216	-0.0458	0.1941	-0.1026	-0.0002	0.1954	0.0343	0.0106	0.2211	-0.005	0.1802	10.8435	8.8155	-27.8806
4	0.0791	-0.095	-0.0603	0.3124	-0.576	0.5572	0.4685	0.8124	0.2788	-0.2438	-0.1888	0.1887	-0.2227	-0.1704	0.0001	0.1934	0.0827	0.0419	0.2411	0.1068	0.2471	10.8496	14.3134	-34.1895
5	1.0846	0.203	0.1116	0.4052	-0.112	0.0571	0.252	-0.6637	0.2929	0.7617	0.1004	0.4106	-0.1848	-0.2416	0.0342	0.2672	0.2338	0.1507	0.3481	0.1984	0.7338	6.6886	22.5696	-25.96
6	0.7166	0.1861	0.0773	0.2017	-0.1391	0.4111	0.1447	0.0872	0.1159	-0.1055	-0.0559	-0.1447	0.047	0.0757	-0	0.1682	0.0359	-0.0023	0.1681	-0.0041	0.1543	35.533	-1.5117	-30.91
7	0.6455	-1.2267	-0.5034	1.2579	0.3858	1.5891	0.1658	0.0623	0.1242	-0.0143	-0.1164	0.1052	0.0054	0.0885	0.0025	0.1811	0.016	0.021	0.153	0.0133	0.1308	37.443	-2.6951	-31.8985
8	0.578	0.6758	0.3669	1.5221	1.0479	0.4043	-0.3938	-0.409	-0.5206	0.009	0.1883	-0.2279	0.3408	0.084	-0.0011	0.1351	0.0537	-0.0035	0.2291	0.0119	0.2022	50.743	-7.5991	-15.4007
9	0.1454	-0.0752	-0.0616	0.6121	0.5069	0.6451	-0.008	0.1139	0.0869	-0.0011	0.0064	0.0473	0.1084	0.1465	0.0001	0.1835	0.007	0.0076	0.2351	-0.0132	0.2342	57.9636	-23.2909	-26.8274
10	0.0877	0.1203	0.0492	0.9145	0.7001	0.4332	-0.2584	-0.3048	0.209	-0.0279	0.3505	-0.348	0.1537	-0.0713	-0	0.1908	0.0201	0.0133	0.2341	-0.0057	0.1798	54.4165	-16.341	-18.2636
11	0.5967	-0.228	0.7572	-0.0109	-0.0633	0.6979	-0.061	-0.5189	0.0032	0.3444	0.3842	-0.3542	0.041	0.3067	0.0001	0.1854	0.0617	-0.0613	0.309	-0.0908	0.3159	60.1124	-14.0524	-12.8574
12	0.0187	-0.0059	-0.0006	-0.0056	-0.0049	-0.0068	0.0237	-0.291	0.1438	-0.5331	0.1551	-0.1444	-0.4018	0.2951	-0.0001	0.1581	-0.0115	0.0587	0.42	-0.0347	0.7453	65.61	-6.8082	-19.0937
13	0.1366	0.0178	0.1303	0.3903	0.1698	0.5341	0.0163	-0.1778	0.1083	0.0218	0.0919	-0.0132	-0.0276	-0.0742	0	0.1376	0.0174	-0.004	0.2158	0.0095	0.1703	31.3657	-0.6984	-14.2321
14	1.6786	-0.2885	-0.472	-0.113	0.1145	1.6088	-0.0499	-0.2032	-0.0317	-0.0367	0.1065	-0.1332	-0.0757	-0.0928	0	0.1316	-0.0005	-0.0041	0.174	-0.0311	0.1385	31.2538	1.4148	-14.5921

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 20:37)
2	X-RAY DIFFRACTION	2	(chain A and resid 38:61)
3	X-RAY DIFFRACTION	3	(chain A and resid 62:83)
4	X-RAY DIFFRACTION	4	(chain A and resid 84:104)
5	X-RAY DIFFRACTION	5	(chain A and resid 105:110)
6	X-RAY DIFFRACTION	6	(chain A and resid 111:142)
7	X-RAY DIFFRACTION	7	(chain A and resid 143:197)
8	X-RAY DIFFRACTION	8	(chain B and resid 20:37)
9	X-RAY DIFFRACTION	9	(chain B and resid 38:61)
10	X-RAY DIFFRACTION	10	(chain B and resid 62:83)
11	X-RAY DIFFRACTION	11	(chain B and resid 84:106)
12	X-RAY DIFFRACTION	12	(chain B and resid 107:112)
13	X-RAY DIFFRACTION	13	(chain B and resid 113:139)
14	X-RAY DIFFRACTION	14	(chain B and resid 140:198)

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