PDB-5nus: Structure of a minimal complex between p44 and p34 from Chaetomiu...

ID or keywords:

Entry

Database: PDB / ID: 5nus

Title

Structure of a minimal complex between p44 and p34 from Chaetomium thermophilum

Components

p34
p44

Keywords

TRANSCRIPTION /

RING finger domain / von Willebrand factor A like

Function / homology

Function and homology information

transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nucleotide-excision repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding /

metal ion binding
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Koelmel, W. / Schoenwetter, E. / Kuper, J. / Schmitt, D.R. / Kisker, C.

Funding support

Germany, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH.
Authors: Radu, L. / Schoenwetter, E. / Braun, C. / Marcoux, J. / Koelmel, W. / Schmitt, D.R. / Kuper, J. / Cianferani, S. / Egly, J.M. / Poterszman, A. / Kisker, C.

History

Deposition	May 2, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5nus.cif.gz	176.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5nus.ent.gz	150 KB	Display	PDB format
PDBx/mmJSON format	5nus.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nu/5nus ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nus	HTTPS FTP

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Related structure data

Related structure data	5o85C 5obzC C: citing same article (ref.)
Similar structure data	1rsz-d 1rt9-d 1i79-d 1rfg-d 1pf7-d 2nzl-d 2q7o-d 1rct-d 1tah-2 3pxn-d 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	#87 - Mar 2007 Zinc Fingers similarity (3) #134 - Feb 2011 Integrin similarity (4) #55 - Jul 2004 DNA Ligase similarity (3) #166 - Oct 2013 Proteasome similarity (3) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (3) #122 - Feb 2010 Enhanceosome similarity (3) #257 - May 2021 Fetal Hemoglobin similarity (3)

Deposited unit

A: p34

B: p44

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	147.056, 147.056, 87.599
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

#1: Protein	p34 Mass: 31972.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Gene: CTHT_0004460 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RXV8
#2: Protein	p44 Mass: 12263.829 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Gene: CTHT_0002690 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZE6
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.09 Å³/Da / Density % sol: 60.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG 4000, MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.14 Å / Num. obs: 28834 / % possible obs: 100 % / Redundancy: 18.5 % / B_iso Wilson estimate: 40.91 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.121 / R_pim(I) all: 0.029 / Net I/σ(I): 19.6
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 14.8 % / R_merge(I) obs: 4.399 / Mean I/σ(I) obs: 1 / Num. unique obs: 2439 / CC_1/2: 0.7 / R_pim(I) all: 1.133 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→41.418 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5

	R_factor	Num. reflection	% reflection
R_free	0.227	1406	4.94 %
R_work	0.2097	-	-
obs	0.2106	28436	98.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 73.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→41.418 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2158	0	2	18	2178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2265
X-RAY DIFFRACTION	f_angle_d	0.728	3093
X-RAY DIFFRACTION	f_dihedral_angle_d	12.52	821
X-RAY DIFFRACTION	f_chiral_restr	0.029	361
X-RAY DIFFRACTION	f_plane_restr	0.003	398

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 (%)
2.2002-2.2788	0.5051	126	0.5191	2337	X-RAY DIFFRACTION	88
2.2788-2.37	0.3673	127	0.3351	2698	X-RAY DIFFRACTION	100
2.37-2.4779	0.2917	141	0.2888	2675	X-RAY DIFFRACTION	100
2.4779-2.6085	0.2774	121	0.2693	2712	X-RAY DIFFRACTION	100
2.6085-2.7719	0.284	122	0.2559	2716	X-RAY DIFFRACTION	100
2.7719-2.9859	0.2456	149	0.2351	2707	X-RAY DIFFRACTION	100
2.9859-3.2862	0.234	156	0.2262	2723	X-RAY DIFFRACTION	100
3.2862-3.7615	0.2154	152	0.1934	2732	X-RAY DIFFRACTION	100
3.7615-4.738	0.1819	141	0.1624	2800	X-RAY DIFFRACTION	100
4.738-41.4258	0.2024	171	0.1774	2930	X-RAY DIFFRACTION	100

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	5.3834	0.8977	-2.729	9.6974	3.1051	4.8516	-0.4178	0.032	-0.3866	0.3069	0.1815	-0.6039	0.539	0.4179	0.5039	0.4332	-0.0658	-0.0513	0.6762	0.0347	0.3475	120.3095	74.5135	8
2	4.1239	-4.6431	-0.9001	9.2341	2.5034	3.0197	-0.306	-0.7986	0.1575	0.2729	0.3804	-0.0357	-0.0903	0.3987	-0.1565	0.4195	-0.1624	-0.0298	0.5796	0.0074	0.4828	120.1995	84.6799	21.1568
3	3.3504	-0.5495	-0.1718	7.5236	0.2011	6.6325	-0.0159	0.1444	0.4196	-0.9908	-0.0566	-0.558	-0.4379	0.4085	0.2067	0.4706	-0.218	-0.0586	0.5394	0.062	0.4522	122.2521	85.6929	8.2586
4	6.7269	4.3748	-4.8807	5.5251	-3.7833	5.1408	-1.1509	0.7575	1.0201	-0.6751	0.6324	-4.1447	-1.0761	2.8684	0.8819	1.13	-0.5268	0.0809	1.3583	0.0952	1.3578	132.22	84.8074	3.2208
5	4.484	-6.5116	-0.6318	6.5162	1.2141	5.7662	0.0748	-0.0935	0.7463	-0.6249	-0.1094	-2.5813	-0.4927	1.1944	-0.1105	0.5483	-0.1936	0.0356	0.8351	0.0248	0.8762	130.6417	85.5053	14.4856
6	4.1178	3.9986	5.6419	5.1794	6.6097	9.5142	-0.1102	0.1396	0.3756	-1.0167	0.2059	-0.6714	-0.2042	-0.0348	-0.2959	0.708	-0.0052	-0.0919	0.6361	-0.0128	0.7866	115.598	100.9301	14.5618
7	5.0362	-0.1338	0.3796	2.8771	0.4078	6.1305	-0.2912	0.3336	0.0329	-1.0986	0.1583	-0.1123	-0.1997	0.7265	0.0523	0.6652	-0.235	0.0208	0.5516	0.0463	0.4042	118.9151	81.4662	-1.4971
8	6.0348	1.3301	-0.4397	9.2958	3.1496	8.2936	-0.0968	0.0037	-0.3504	-1.3264	-0.4051	0.369	-0.3531	-0.1507	0.2708	0.4982	-0.1244	-0.0698	0.5055	0.1318	0.423	116.8354	76.9957	4.5448
9	8.0581	-6.1069	0.2671	7.7214	1.6237	6.8177	-0.3433	0.3294	0.4771	-0.118	-0.4894	0.4159	-0.3641	-0.7813	0.7065	0.6509	-0.1628	-0.1913	0.7237	-0.0382	0.524	105.8073	85.0163	0.5264
10	6.0334	6.7348	3.7941	4.029	4.4759	4.125	-0.3275	-0.7418	0.5517	-0.6711	-0.8012	1.2728	-0.5058	-2.349	0.8371	0.4689	0.0519	-0.1504	0.847	-0.1507	0.5498	105.4121	83.0457	12.9701
11	8.914	3.9006	7.2328	6.666	5.1811	6.8359	-0.0549	-0.9248	-0.0583	0.4128	-0.1556	0.6824	0.7492	-2.3135	0.2115	0.4194	-0.13	0.0781	0.838	0.0559	0.5063	105.9782	78.1155	17.2329
12	8.5911	-5.53	-4.9619	10.0914	1.5476	3.6732	-0.5197	-0.7627	-0.19	0.6061	0.534	-0.1703	-0.0045	1.2093	0.2511	0.4927	-0.1172	0.0171	0.6097	0.0991	0.463	115.2533	76.5016	23.228
13	5.0859	2.5631	-2.1705	6.7438	-3.1427	6.6147	-0.4945	1.6027	-0.3513	-0.2026	0.3185	-0.003	-0.7043	-0.2413	0.1547	1.2862	-0.2326	-0.2046	0.8794	0.218	0.6675	115.8415	94.5527	-13.5545
14	4.2729	-0.0001	-1.6592	3.3391	-1.5651	1.3944	0.0342	-0.7132	0.961	-0.7836	-0.0238	-1.002	-1.1781	2.1628	0.0865	1.2427	-0.706	0.0796	1.2134	0.0663	0.7813	130.3986	93.8454	-8.2643
15	2.375	2.9851	-3.5308	3.9435	-5.0194	7.3522	2.3263	-0.5976	0.5093	-1.7255	-0.9928	-1.5629	-0.665	2.1369	-1.0809	2.4643	-0.3169	0.4043	1.5931	-0.172	1.7445	138.1059	89.0442	-16.6167
16	5.6434	0.1456	-3.1098	5.9656	-2.0077	6.1042	-0.1328	1.0651	0.2929	-1.6054	0.0641	0.0451	-1.2721	-0.0897	-0.2237	1.3193	-0.4176	-0.0592	0.7698	0.0988	0.4425	119.3206	90.7934	-10.418
17	5.7607	1.1761	-3.0455	8.9521	3.8324	4.2806	0.6167	0.0412	1.215	-0.6912	-0.6078	0.3446	-1.477	-0.9227	-0.3164	0.989	-0.1738	-0.1825	0.4356	0.1037	0.6968	115.6266	98.6062	1.1727

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 62 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 63 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 126 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 127 through 141 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 142 through 161 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 162 through 212 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 213 through 232 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 233 through 252 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 253 through 262 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 263 through 274 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 380 through 389 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 390 through 409 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 410 through 414 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 415 through 444 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 445 through 453 )

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