PDB-5ol8: Structure of human mitochondrial transcription elongation factor ...

ID or keywords:

Entry

Database: PDB / ID: 5ol8

Title

Structure of human mitochondrial transcription elongation factor (TEFM) C-terminal domain

Components

Transcription elongation factor, mitochondrial

Keywords

TRANSCRIPTION / Elongation Factor / Mitochondria / Resolvase / RNA Polymerase

Function / homology

Function and homology information

transcription elongation by mitochondrial RNA polymerase / mitochondrial transcription / oxidative phosphorylation / DNA polymerase processivity factor activity / mitochondrial nucleoid / mitochondrial matrix / ribonucleoprotein complex / mitochondrion / RNA binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Hillen, H.S. / Parshin, A.V. / Agaronyan, K. / Morozov, Y. / Graber, J.J. / Chernev, A. / Schwinghammer, K. / Urlaub, H. / Anikin, M. / Cramer, P. / Temiakov, D.

Funding support

United States,

Germany, 5items

Organization	Grant number	Country
National Institutes of Health	RO1 GM104231	United States
German Research Foundation	SFB860	Germany
German Research Foundation	SPP1935	Germany
European Research Council	693023	Germany
Volkswagen Foundation		Germany

Citation

Journal: Cell / Year: 2017
Title: Mechanism of Transcription Anti-termination in Human Mitochondria.
Authors: Hillen, H.S. / Parshin, A.V. / Agaronyan, K. / Morozov, Y.I. / Graber, J.J. / Chernev, A. / Schwinghammer, K. / Urlaub, H. / Anikin, M. / Cramer, P. / Temiakov, D.

History

Deposition	Jul 27, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Nov 29, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ol8.cif.gz	359.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ol8.ent.gz	295.8 KB	Display	PDB format
PDBx/mmJSON format	5ol8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ol8_validation.pdf.gz	471.8 KB	Display	wwPDB validaton report
Full document	5ol8_full_validation.pdf.gz	477 KB	Display
Data in XML	5ol8_validation.xml.gz	30.2 KB	Display
Data in CIF	5ol8_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ol/5ol8 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5ol8	HTTPS FTP

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Related structure data

Related structure data	5ol9C 5olaC C: citing same article (ref.)
Similar structure data	5lhp-d 6qwn-4 6bcf-2 5lhq-d 6fb0-d 4z1x-1 6bch-3 3mxa-d 6bcg-2 6fb9-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	#40 - Apr 2003 RNA Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #55 - Jul 2004 DNA Ligase similarity (1)

Deposited unit

A: Transcription elongation factor, mitochondrial

B: Transcription elongation factor, mitochondrial

C: Transcription elongation factor, mitochondrial

D: Transcription elongation factor, mitochondrial

hetero molecules

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

1

A: Transcription elongation factor, mitochondrial

B: Transcription elongation factor, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration
74.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Transcription elongation factor, mitochondrial

D: Transcription elongation factor, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration, Homodimer.
74.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.480, 112.540, 88.840
Angle α, β, γ (deg.)	90.00, 110.13, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-527- HOH

#1: Protein	Transcription elongation factor, mitochondrial Mass: 37187.785 Da / Num. of mol.: 4 / Fragment: UNP Residues 51-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEFM, C17orf42 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q96QE5
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.12 Å³/Da / Density % sol: 42.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Limited proteolysis with ArgC at RT for 20min. BIS-TRIS pH 5.5-6.5, MgCl2, PEG3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 1.0, 0.9765

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.9765	1

Reflection

Resolution: 1.9→46.233 Å / Num. obs: 70199 / % possible obs: 98.1 % / Redundancy: 6.6 % / CC_1/2: 1 / R_merge(I) obs: 0.051 / Net I/σ(I): 17.92

Reflection shell

Resolution: 1.9→1.94 Å / Redundancy: 5.04 % / R_merge(I) obs: 2.49 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 4740 / CC_1/2: 0.35 / % possible all: 89.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→46.233 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.34

	R_factor	Num. reflection	% reflection
R_free	0.2278	3503	5 %
R_work	0.1954	-	-
obs	0.197	70119	98.06 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→46.233 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6724	0	24	129	6877

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6888
X-RAY DIFFRACTION	f_angle_d	0.506	9276
X-RAY DIFFRACTION	f_dihedral_angle_d	15.474	4156
X-RAY DIFFRACTION	f_chiral_restr	0.041	1036
X-RAY DIFFRACTION	f_plane_restr	0.002	1156

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 (%)
1.9-1.926	0.4633	125	0.4829	2406	X-RAY DIFFRACTION	88
1.926-1.9535	0.5173	128	0.4538	2439	X-RAY DIFFRACTION	91
1.9535-1.9827	0.4105	136	0.4315	2575	X-RAY DIFFRACTION	95
1.9827-2.0136	0.4505	142	0.4279	2701	X-RAY DIFFRACTION	99
2.0136-2.0467	0.4113	142	0.3814	2688	X-RAY DIFFRACTION	99
2.0467-2.0819	0.3614	141	0.3518	2683	X-RAY DIFFRACTION	99
2.0819-2.1198	0.3581	140	0.3042	2672	X-RAY DIFFRACTION	99
2.1198-2.1606	0.3073	141	0.2832	2675	X-RAY DIFFRACTION	99
2.1606-2.2047	0.3037	142	0.2907	2695	X-RAY DIFFRACTION	99
2.2047-2.2526	0.3657	140	0.2704	2660	X-RAY DIFFRACTION	99
2.2526-2.305	0.293	140	0.2619	2649	X-RAY DIFFRACTION	98
2.305-2.3627	0.3091	141	0.2473	2680	X-RAY DIFFRACTION	99
2.3627-2.4265	0.2962	143	0.2347	2717	X-RAY DIFFRACTION	99
2.4265-2.4979	0.2699	141	0.2368	2702	X-RAY DIFFRACTION	99
2.4979-2.5785	0.2814	141	0.2273	2694	X-RAY DIFFRACTION	99
2.5785-2.6707	0.2626	142	0.2264	2699	X-RAY DIFFRACTION	99
2.6707-2.7776	0.2578	141	0.2089	2666	X-RAY DIFFRACTION	98
2.7776-2.904	0.2838	140	0.2187	2664	X-RAY DIFFRACTION	98
2.904-3.0571	0.2215	142	0.2158	2706	X-RAY DIFFRACTION	100
3.0571-3.2486	0.2334	143	0.2032	2710	X-RAY DIFFRACTION	100
3.2486-3.4993	0.2169	142	0.1904	2692	X-RAY DIFFRACTION	99
3.4993-3.8513	0.2066	139	0.1756	2670	X-RAY DIFFRACTION	98
3.8513-4.4082	0.2108	144	0.148	2735	X-RAY DIFFRACTION	100
4.4082-5.5524	0.1603	141	0.1424	2685	X-RAY DIFFRACTION	98
5.5524-46.2464	0.1723	146	0.159	2753	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	0.7232	0.9535	-0.0989	1.4816	0.1156	0.2928	0.3742	-1.0593	0.4891	0.8964	-0.3539	0.7183	-0.4451	-0.6585	-0.0046	0.8989	-0.0857	0.1262	0.9508	-0.0184	0.5803	-4.6639	98.2854	-10.5554
2	2.5835	1.2242	0.2953	2.3476	0.6792	0.1362	0.4668	-0.1726	-0.4027	0.3089	0.1791	-0.7642	-0.4961	0.2852	-0.0009	0.443	-0.049	-0.0193	0.4772	0.0488	0.5584	9.6316	97.6402	-23.3098
3	1.2563	1.0278	0.3803	3.0229	-0.4594	0.3882	0.4199	-0.0623	-0.1869	0.6592	-0.1184	-0.9821	0.3892	-0.1146	0.0002	0.541	-0.1497	-0.1439	0.694	0.0591	0.9467	14.5754	99.1151	-17.1483
4	0.3863	0.0673	-0.2537	0.3877	-0.1712	0.1269	0.2587	0.3315	-1.1768	-0.3773	-0.026	-0.1774	0.2057	0.4367	0	0.787	-0.0357	0.112	0.7044	0.0108	0.6309	8.4449	91.56	-40.1461
5	1.0031	0.8039	-0.3176	3.7944	2.2123	3.9667	0.0214	-0.0602	0.0338	0.1489	0.028	-0.56	-0.1378	-0.1457	0.0005	0.4512	-0.0149	-0.0144	0.5079	0.0624	0.5752	3.9317	92.5795	-26.9882
6	2.8482	1.4824	-0.8838	1.5915	0.8633	1.9655	-0.3224	0.0826	0.3601	-0.7049	0.4116	0.2288	-0.747	-0.1104	0.0008	0.5869	-0.0832	-0.0284	0.4418	0.0448	0.5062	-0.9436	94.3576	-32.8903
7	3.0039	0.7934	0.076	1.3319	1.3541	1.733	0.1911	-0.3087	0.3079	0.4828	-0.2057	0.3169	-0.2908	-0.3651	0.0002	0.6001	-0.0091	-0.0323	0.5717	0.0046	0.495	-0.0503	102.0365	-20.9425
8	0.5003	0.6194	0.3756	0.4753	0.4782	0.4949	0.0529	-0.5192	0.3547	0.8147	0.217	-0.6562	-1.3775	0.6513	0.0032	0.9735	-0.2355	-0.1484	0.8018	0.0067	1.0507	17.6997	112.2832	-14.2379
9	0.6762	-1.1372	0.6847	3.9366	-0.2615	1.5818	0.0817	0.3947	-0.1611	-0.6496	0.2611	-2.4534	-0.0726	1.1663	0.009	0.5337	-0.2099	0.0275	0.8215	-0.0916	1.368	22.5923	104.6868	-23.3348
10	1.9001	1.2306	1.4671	3.5211	0.6419	1.2373	-0.0195	-0.1079	0.2857	0.3086	-0.0587	-0.295	-0.4886	-0.7976	-0.0002	0.6072	-0.0592	-0.1116	0.5309	0.0187	0.5717	6.4201	105.2921	-17.1265
11	2.5569	1.5951	1.7688	3.9561	0.6553	4.5353	0.2664	0.0198	-0.5881	-0.32	-0.1106	-0.2136	0.7481	-0.0215	0	0.5528	-0.0239	0.0097	0.4742	0.0193	0.5562	-5.7771	69.3206	-37.1827
12	0.1203	-0.3294	-0.3184	0.4473	0.4023	0.438	-0.3518	-0.9353	0.5758	-0.1447	-0.2203	1.4926	0.1582	-1.1929	-0.0005	0.6417	0.0491	0.0109	0.8684	-0.0729	0.7251	-17.4349	88.1526	-29.7497
13	1.6104	1.3223	1.5118	3.0728	1.7729	2.6501	-0.068	-0.0241	0.0584	-0.3597	-0.0336	-0.1186	-0.0598	-0.2514	-0.0001	0.4289	-0.0358	0.0307	0.4537	0.0277	0.4662	-7.1182	83.1681	-34.0064
14	3.0901	1.7195	-0.3889	2.5306	1.7834	1.7932	0.0451	0.5696	-0.3637	-0.3536	0.0298	-0.0396	0.1936	0.1691	0.0005	0.5388	-0.0194	-0.0183	0.492	0.0339	0.5277	-4.9034	74.6645	-43.2593
15	0.1056	0.6922	0.7403	0.6947	0.8247	0.568	0.1476	0.1446	-0.2074	0.0814	-0.3789	0.1735	0.2006	-0.6319	-0.0001	0.7913	-0.1529	-0.0921	0.7831	-0.0392	0.7581	-19.5344	58.9408	-44.8637
16	3.1487	2.3876	2.2787	4.4344	0.5247	6.0697	0.1128	-0.3849	0.0719	0.1871	-0.2634	0.2318	0.5664	-1.2165	-0.0001	0.5568	-0.144	-0.0125	0.6647	-0.0363	0.5552	-17.156	67.1775	-39.1044
17	4.1004	0.2108	-0.3628	4.8222	-2.5778	3.7718	0.0554	-0.1939	0.326	0.3398	-0.2008	0.0205	-0.6025	-0.019	0.0001	0.5454	-0.0034	0.0264	0.5041	-0.0063	0.4969	-39.9717	131.92	-79.045
18	1.9015	-0.3384	0.237	1.9711	-0.5416	1.1863	0.0952	1.3336	-0.1123	-1.8336	-0.149	-0.0809	0.5876	0.9107	0.0003	0.812	-0.0109	0.0928	0.7605	0.125	0.6891	-28.4825	115.7493	-84.2622
19	2.6866	-2.4108	0.4665	3.2491	-2.259	2.7819	0.2454	-0.2507	0.1375	-0.2216	-0.1936	0.1703	-0.0469	-0.2278	-0	0.4872	-0.0337	0.0273	0.4998	0.0562	0.4891	-38.9986	119.8194	-75.9279
20	1.844	-1.1319	0.7289	1.3116	-2.2985	3.1514	0.1415	0.1326	0.1523	-0.4258	0.061	0.3222	-0.1055	-0.5087	0.0001	0.6897	0.0613	-0.0114	0.6043	0.0067	0.5861	-48.0434	134.3282	-90.3321
21	2.8668	-0.4688	0.3967	4.3626	-2.6022	3.3352	0.2736	0.303	0.0305	-0.3986	-0.4101	-0.1423	0.1802	0.1018	0	0.5445	0.0713	0.0632	0.4995	0.0383	0.4913	-39.5921	133.7314	-90.5976
22	3.7025	-1.7703	2.2637	6.0322	-0.1789	3.1563	-0.13	-0.0053	0.1174	0.2458	0.0326	-0.8145	-0.0086	0.1258	-0.0039	0.497	-0.0569	-0.013	0.5663	0.0639	0.5599	-22.5177	102.9984	-63.1136
23	3.1689	-2.2328	1.5993	5.9613	-2.139	2.3118	-0.1483	-0.4202	0.092	0.4038	0.2567	0.133	0.1401	-0.2611	-0.0004	0.5691	-0.0618	0.0555	0.6043	0.0316	0.4622	-36.0846	108.7201	-66.1244
24	2.4406	-1.8964	1.7754	4.2536	-2.1371	2.8496	-0.0032	0.0484	0.1072	-0.2459	-0.0557	-0.3257	-0.0318	0.2048	-0.0002	0.4937	-0.0727	0.0636	0.5028	0.0606	0.4836	-29.5118	106.4308	-71.9015
25	3.0705	-2.0221	-1.1838	2.1082	0.4755	0.8721	0.1099	-0.7205	-0.8394	0.2349	0.1039	-0.5462	0.8152	-0.2183	-0	0.9108	-0.161	-0.0852	0.7976	0.2269	0.7321	-25.5101	88.0803	-56.4039
26	3.5726	0.8983	2.2838	2.9038	1.867	2.3869	0.2012	-1.785	0.4026	1.0361	-0.207	0.5656	0.0161	-1.15	-0.1342	1.0007	-0.1645	-0.0186	1.3938	0.1205	0.4478	-33.451	96.5089	-48.564
27	0.6796	-0.2111	1.2444	3.1753	0.0901	2.0908	0.2696	0.1034	-0.0831	0.1536	-0.0972	-0.3909	0.0637	-0.0292	-0.0002	0.4953	0.0116	-0.0512	0.532	0.0553	0.5073	-23.0536	96.0617	-62.5471

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 153 through 168 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 169 through 186 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 187 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 208 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 209 through 240 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 241 through 261 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 262 through 296 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 297 through 318 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 319 through 337 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 338 through 357 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 153 through 196 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 197 through 208 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 209 through 261 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 262 through 296 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 297 through 318 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 319 through 357 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 153 through 196 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 197 through 222 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 223 through 272 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 273 through 318 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 319 through 357 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 153 through 196 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 197 through 240 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 241 through 284 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 285 through 318 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 319 through 337 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 338 through 357 )

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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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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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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

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi