PDB-3hfh: Crystal structure of tandem FF domains

ID or keywords:

Entry

Database: PDB / ID: 3hfh

Title

Crystal structure of tandem FF domains

Components

Transcription elongation regulator 1

Keywords

TRANSCRIPTION REGULATOR /

helix bundle / Activator /

Alternative splicing /

Coiled coil /

Nucleus /

Phosphoprotein /

Repressor /

Transcription /

Transcription regulation

Function / homology

Function and homology information

transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding /

RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway /

RNA splicing / positive regulation of transcription elongation by RNA polymerase II /

transcription coregulator activity /

mRNA processing / transcription corepressor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.703 Å

Authors

Lu, M. / Yang, J. / Ren, Z. / Subir, S. / Bedford, M.T. / Jacobson, R.H. / McMurray, J.S. / Chen, X.

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the Three Tandem FF Domains of the Transcription Elongation Regulator CA150.
Authors: Lu, M. / Yang, J. / Ren, Z. / Sabui, S. / Espejo, A. / Bedford, M.T. / Jacobson, R.H. / Jeruzalmi, D. / McMurray, J.S. / Chen, X.

History

Deposition	May 11, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 18, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hfh.cif.gz	171.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3hfh.ent.gz	151.9 KB	Display	PDB format
PDBx/mmJSON format	3hfh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hf/3hfh ftp://data.pdbj.org/pub/pdb/validation_reports/hf/3hfh	HTTPS FTP

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Related structure data

Similar structure data	1qz1-d 2nzi-1 2nzi-2 5h7b-1 619 3ov0-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	#245 - May 2020 Spliceosomes similarity (11) #130 - Oct 2010 Riboswitches similarity (1) #65 - May 2005 Self-splicing RNA similarity (1)

Deposited unit

A: Transcription elongation regulator 1

B: Transcription elongation regulator 1

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

1

A: Transcription elongation regulator 1

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

2

B: Transcription elongation regulator 1

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

Unit cell

Length a, b, c (Å)	141.300, 141.300, 155.420
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	177
Space group name H-M	P622

#1: Protein	Transcription elongation regulator 1 / / TATA box-binding protein-associated factor 2S / Transcription factor CA150 Mass: 23830.676 Da / Num. of mol.: 2 / Fragment: FF domains: UNP residues 661-845 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA150, TAF2S, TCERG1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O14776
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Transcription elongation regulator 1 /

/ TATA box-binding protein-associated factor 2S / Transcription factor CA150

Mass: 23830.676 Da / Num. of mol.: 2 / Fragment: FF domains: UNP residues 661-845
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CA150, TAF2S, TCERG1 / Plasmid: pGEX-6P-1 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O14776

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.7 Å³/Da / Density % sol: 73.82 % Description: The structure factor file contains Friedel pairs
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM Bis-Tris pH 6.5, 50 mM Ammonium sulfate, 30% Pentaerythritol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.7→20.016 Å / Num. obs: 44246 / % possible obs: 99.9 % / Redundancy: 11.7 % / R_merge(I) obs: 0.109 / Net I/σ(I): 34.703
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 11.2 % / R_merge(I) obs: 0.563 / % possible all: 100

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Phasing

Phasing	Method: SAD
Phasing MAD	D res high: 2.7 Å / D res low: 20.02 Å / FOM : 0.452 / FOM acentric: 0.516 / FOM centric: 0.244 / Reflection: 24629 / Reflection acentric: 19611 / Reflection centric: 3435

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.703→20.016 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.26 / σ(F): 0.08 / Phase error: 29.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing and refinement

	R_factor	Num. reflection	% reflection
R_free	0.2833	4331	9.8 %
R_work	0.23	-	-
obs	0.2353	44209	93.15 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.315 Å² / k_sol: 0.263 e/Å³

Displacement parameters

B_iso mean: 90.966 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.099 Å²	-0 Å²	-0 Å²
2-	-	-5.099 Å²	0 Å²
3-	-	-	-23.281 Å²

Refinement step

Cycle: LAST / Resolution: 2.703→20.016 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3123	0	0	55	3178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3177
X-RAY DIFFRACTION	f_angle_d	1.153	4236
X-RAY DIFFRACTION	f_dihedral_angle_d	19.452	1286
X-RAY DIFFRACTION	f_chiral_restr	0.076	408
X-RAY DIFFRACTION	f_plane_restr	0.005	581

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 (%)
2.703-2.7338	0.3412	144	0.271	1135	X-RAY DIFFRACTION	80
2.7338-2.7659	0.3451	130	0.268	1171	X-RAY DIFFRACTION	82
2.7659-2.7995	0.315	119	0.2602	1183	X-RAY DIFFRACTION	82
2.7995-2.8349	0.3013	133	0.2647	1165	X-RAY DIFFRACTION	83
2.8349-2.8721	0.3225	119	0.2589	1212	X-RAY DIFFRACTION	83
2.8721-2.9113	0.3485	140	0.2738	1218	X-RAY DIFFRACTION	85
2.9113-2.9528	0.3234	123	0.2478	1237	X-RAY DIFFRACTION	87
2.9528-2.9967	0.2987	132	0.2559	1264	X-RAY DIFFRACTION	88
2.9967-3.0434	0.3442	107	0.2789	1279	X-RAY DIFFRACTION	88
3.0434-3.0931	0.3071	149	0.2687	1261	X-RAY DIFFRACTION	90
3.0931-3.1462	0.3644	124	0.259	1307	X-RAY DIFFRACTION	92
3.1462-3.2032	0.3037	143	0.2691	1334	X-RAY DIFFRACTION	94
3.2032-3.2646	0.2789	145	0.2498	1380	X-RAY DIFFRACTION	96
3.2646-3.3309	0.3108	133	0.2617	1387	X-RAY DIFFRACTION	96
3.3309-3.403	0.3122	145	0.2609	1393	X-RAY DIFFRACTION	98
3.403-3.4818	0.3089	144	0.2597	1391	X-RAY DIFFRACTION	97
3.4818-3.5684	0.2947	152	0.2138	1388	X-RAY DIFFRACTION	98
3.5684-3.6643	0.2858	147	0.2179	1397	X-RAY DIFFRACTION	97
3.6643-3.7714	0.2849	162	0.2099	1368	X-RAY DIFFRACTION	97
3.7714-3.8923	0.2324	162	0.1919	1408	X-RAY DIFFRACTION	98
3.8923-4.0303	0.2428	142	0.1832	1400	X-RAY DIFFRACTION	98
4.0303-4.1903	0.2438	158	0.1936	1376	X-RAY DIFFRACTION	98
4.1903-4.3791	0.2173	138	0.186	1418	X-RAY DIFFRACTION	98
4.3791-4.6073	0.1981	167	0.1842	1403	X-RAY DIFFRACTION	99
4.6073-4.892	0.2473	169	0.1787	1408	X-RAY DIFFRACTION	99
4.892-5.2634	0.2836	149	0.1799	1411	X-RAY DIFFRACTION	99
5.2634-5.7814	0.2756	162	0.2021	1406	X-RAY DIFFRACTION	99
5.7814-6.5917	0.2717	143	0.2059	1426	X-RAY DIFFRACTION	99
6.5917-8.2085	0.2948	182	0.2456	1393	X-RAY DIFFRACTION	100
8.2085-20.016	0.2722	168	0.2511	1359	X-RAY DIFFRACTION	96

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	0.0073	-0.6097	-0.1811	-0.0709	0.6859	0.8146	0.0377	0.4968	0.5378	-0.2824	0.1544	0.1086	-0.0385	-0.4631	-0.0001	0.5725	-0.0049	0.0055	0.6069	0.093	0.6951	17.204	53.042	116.9616
2		1.9688	1.1807	0.1237	1.1866	0.0958	1.5433	-0.0342	0.1571	0.2778	-0.0259	0.1231	-0.097	0.5462	0.2798	-0.0001	0.6229	0.0423	-0.0171	0.5884	0.0582	0.5048
3		-0.3134	-0.5328	0.0753	0.1979	-0.1359	0.4488	0.3119	0.1819	0.0428	-0.518	0.229	0.5121	0.5033	-0.5996	0	0.5686	0.0421	-0.1208	0.8957	0.1404	0.6256
4		-0.1754	0.1322	-0.1684	0.337	-0.2071	0.1915	0.4239	-0.7878	-2.004	-1.0058	0.3311	0.3921	-0.9356	2.0485	0.0042	1.2116	0.0065	-0.1001	1.1306	0.2199	0.7161
5		-0.069	0.1124	0.109	0.0296	0.0201	0.2156	-0.6886	-1.0111	0.308	0.5858	-1.0291	0.5518	-1.0713	-1.442	0.0108	1.4373	0.1352	-0.0348	2.0947	0.0842	1.0025
6		0.467	0.4581	-0.4788	0	0.2496	0.8288	0.8879	0.6918	-0.1278	-0.2341	-0.2397	-0.2695	-0.5454	-1.6978	0.0014	1.8542	0.6375	0.3432	1.7318	0.208	0.927
7		0.1048	-0.241	-0.3192	-0.1227	-0.2021	-0.1466	-1.7974	-2.0507	-1.2474	-0.754	0.9729	1.4648	1.0822	0.864	0.0005	1.8286	0.4601	-0.0358	1.7671	-0.0349	1.3874
8		1.4716	1.2612	-1.1643	1.9612	0.7064	1.5091	-0.3215	-0.271	0.3711	0.2429	0.4612	0.1446	0.0399	-0.1324	0.0001	0.7471	0.1378	-0.1235	0.9128	-0.1363	0.6922
9		0.2813	-0.0476	0.0889	0.2932	0.3949	1.1417	-0.6149	1.133	1.1344	0.1659	0.927	-1.6541	-1.6272	3.1543	0.0207	0.7389	-0.0697	-0.1522	1.1055	-0.1368	1.2548
10		0.1838	0.067	0.2305	0.0497	0.0835	0.3368	-0.0261	1.4926	-0.3348	-0.9522	-0.1249	0.9074	0.9288	0.5023	0.0007	0.8071	0.1027	-0.0162	0.8013	-0.2229	0.7634
11		1.6557	0.7159	0.8602	0.9867	-0.8271	2.7232	-0.1372	0.0814	-0.1202	0.1367	-0.1402	0.0751	0.0847	-0.1243	0.0002	0.4102	0.0098	0.0498	0.4474	-0.0131	0.4762
12		-0.7639	-1.8077	-1.3281	0.4919	-0.2922	1.2829	0.1157	0.2237	0.114	0.1555	0.6838	0.4917	-0.3059	-0.7878	0.0011	0.4495	0.0523	0.0548	0.5867	-0.0248	0.5189
13		0.0404	0.8836	-0.3386	0.0001	-0.0722	0.2368	0.4817	0.5412	0.1712	-0.5544	-0.3404	0.0307	-1.0989	-2.755	0.0001	0.6335	0.1723	0.0278	1.3202	0.1536	0.5146
14		0.3386	0.5408	0.6531	1.0245	0.8331	0.5817	-3.7275	0.7222	-1.2412	-1.7468	-0.2689	1.5965	0.1995	-0.5772	-0.0309	1.1988	0.2376	0.0322	1.696	0.206	0.8583
15		1.568	-1.8113	1.1486	1.9897	-0.3395	0.849	0.083	0.2893	-0.0596	-0.027	0.0055	0.2144	-0.0994	0.0726	-0	0.5114	-0.0761	0.0879	0.5003	0.0361	0.5391
16		0.2169	-0.4143	-0.4364	0.2832	0.3968	-0.1414	0.4718	0.0769	0.6574	0.5478	-0.2048	0.2348	-0.2785	-0.1315	0.0004	0.7588	0.2037	0.1032	0.7314	0.0367	0.7685
17		0.319	-0.0422	-0.1889	0.0086	0.0087	0.0212	0.9675	1.5875	0.1363	0.9062	-0.0399	-0.45	-0.7892	-0.4945	-0.0014	0.7393	0.1982	0.1393	0.7156	-0.0251	0.9126
18		-0.0016	0.0453	-0.3326	0.2605	-0.7235	0.2171	0.1834	-0.0297	-1.2989	0.315	-0.3075	1.4713	0.9882	-3.1821	-0.0075	0.6405	0.1226	-0.0025	1.0032	-0.0143	0.691
19		0.0635	0.3277	-0.6574	1.4059	0.0102	0.0557	-0.1492	0.4973	-1.8028	0.6715	0.0091	0.2158	0.8502	-0.8856	0.0022	0.765	0.0299	0.0472	0.7551	-0.0081	1.2681
20		0.4518	0.1211	-0.7885	0.5897	-0.334	2.6724	0.8409	-1.1915	-0.8371	1.0659	-0.2557	-0.1776	-0.9102	0.5258	0.0487	0.5226	-0.0381	-0.2249	0.7999	0.0828	0.7591

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 656:672)	A	656 - 672
2	X-RAY DIFFRACTION	2	(chain A and resid 673:698)	A	673 - 698
3	X-RAY DIFFRACTION	3	(chain A and resid 699:712)	A	699 - 712
4	X-RAY DIFFRACTION	4	(chain A and resid 713:717)	A	713 - 717
5	X-RAY DIFFRACTION	5	(chain A and resid 718:721)	A	718 - 721
6	X-RAY DIFFRACTION	6	(chain A and resid 722:776)	A	722 - 776
7	X-RAY DIFFRACTION	7	(chain A and resid 777:793)	A	777 - 793
8	X-RAY DIFFRACTION	8	(chain A and resid 794:813)	A	794 - 813
9	X-RAY DIFFRACTION	9	(chain A and resid 814:836)	A	814 - 836
10	X-RAY DIFFRACTION	10	(chain A and resid 837:845)	A	837 - 845
11	X-RAY DIFFRACTION	11	(chain B and resid 656:697)	B	656 - 697
12	X-RAY DIFFRACTION	12	(chain B and resid 698:724)	B	698 - 724
13	X-RAY DIFFRACTION	13	(chain B and resid 725:738)	B	725 - 738
14	X-RAY DIFFRACTION	14	(chain B and resid 739:744)	B	739 - 744
15	X-RAY DIFFRACTION	15	(chain B and resid 745:774)	B	745 - 774
16	X-RAY DIFFRACTION	16	(chain B and resid 775:791)	B	775 - 791
17	X-RAY DIFFRACTION	17	(chain B and resid 792:801)	B	792 - 801
18	X-RAY DIFFRACTION	18	(chain B and resid 802:813)	B	802 - 813
19	X-RAY DIFFRACTION	19	(chain B and resid 814:834)	B	814 - 834
20	X-RAY DIFFRACTION	20	(chain B and resid 835:845)	B	835 - 845

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