PDB-6ero: Structure of human TFB2M

ID or keywords:

Entry

Database: PDB / ID: 6ero

Title

Structure of human TFB2M

Components

Dimethyladenosine transferase 2, mitochondrial,Dimethyladenosine transferase 2, mitochondrial

Keywords

TRANSCRIPTION /

Mitochondria / Initiation /

Polymerase

Function / homology

Function and homology information

Mitochondrial transcription initiation / mitochondrial transcription factor activity /

transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / mitochondrial transcription / rRNA methylation / mitochondrial nucleoid /

Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis /

mitochondrial matrix ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Hillen, H.S. / Morozov, Y.I. / Sarfallah, A. / Temiakov, D. / Cramer, P.

Funding support

Germany,

United States, 6items

Organization	Grant number	Country
German Research Foundation	SFB860	Germany
German Research Foundation	SPP1935	Germany
European Research Council	693023	Germany
Volkswagen Foundation		Germany
National Institutes of Health	RO1 GM104231	United States
Boehringer Ingelheim Fonds	PhD Student Fellowship	Germany

Citation

Journal: Cell / Year: 2017
Title: Structural Basis of Mitochondrial Transcription Initiation.
Authors: Hillen, H.S. / Morozov, Y.I. / Sarfallah, A. / Temiakov, D. / Cramer, P.

History

Deposition	Oct 18, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 31, 2018	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ero.cif.gz	347.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6ero.ent.gz	302.6 KB	Display	PDB format
PDBx/mmJSON format	6ero.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/er/6ero ftp://data.pdbj.org/pub/pdb/validation_reports/er/6ero	HTTPS FTP

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Related structure data

Related structure data	6erpC 6erqC C: citing same article (ref.)
Similar structure data	2w5k-d 3zev-1 6ckw-d 3i7d-d 3w9f-1 6chp-d 6kfd-1 4mcj-5 6cck-d 3syn-2 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

Deposited unit

A: Dimethyladenosine transferase 2, mitochondrial,Dimethyladenosine transferase 2, mitochondrial

B: Dimethyladenosine transferase 2, mitochondrial,Dimethyladenosine transferase 2, mitochondrial

hetero molecules

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

1

A: Dimethyladenosine transferase 2, mitochondrial,Dimethyladenosine transferase 2, mitochondrial

hetero molecules

defined by author
Evidence: gel filtration
35.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dimethyladenosine transferase 2, mitochondrial,Dimethyladenosine transferase 2, mitochondrial

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.950, 165.650, 44.730
Angle α, β, γ (deg.)	90.00, 97.97, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Dimethyladenosine transferase 2, mitochondrial,Dimethyladenosine transferase 2, mitochondrial / Hepatitis C virus NS5A-transactivated protein 5 / HCV NS5A-transactivated protein 5 / Mitochondrial ...Hepatitis C virus NS5A-transactivated protein 5 / HCV NS5A-transactivated protein 5 / Mitochondrial 12S rRNA dimethylase 2 / Mitochondrial transcription factor B2 / mtTFB2 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 2 Mass: 35717.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TFB2M, NS5ATP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: Q9H5Q4, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.26 Å³/Da / Density % sol: 45.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NaCl, PEG3350, HEPES

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→43.53 Å / Num. obs: 62109 / % possible obs: 97.8 % / Redundancy: 7.1 % / CC_1/2: 1 / R_rim(I) all: 0.048 / Net I/σ(I): 20.17
Reflection shell	Resolution: 1.75→1.79 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.75 / Num. unique obs: 4544 / CC_1/2: 0.377 / R_rim(I) all: 2.874 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Truncated model of S.cerevisiae Mtf1

Resolution: 1.75→43.525 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.07

	R_factor	Num. reflection	% reflection
R_free	0.2138	3103	5 %
R_work	0.192	-	-
obs	0.1931	62090	97.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→43.525 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4627	0	14	297	4938

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4744
X-RAY DIFFRACTION	f_angle_d	0.68	6400
X-RAY DIFFRACTION	f_dihedral_angle_d	14.444	2871
X-RAY DIFFRACTION	f_chiral_restr	0.045	707
X-RAY DIFFRACTION	f_plane_restr	0.004	806

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 (%)
1.7501-1.7774	0.378	140	0.3601	2651	X-RAY DIFFRACTION	98
1.7774-1.8065	0.3569	138	0.3514	2663	X-RAY DIFFRACTION	97
1.8065-1.8377	0.3638	138	0.3336	2628	X-RAY DIFFRACTION	96
1.8377-1.8711	0.3359	133	0.3098	2520	X-RAY DIFFRACTION	92
1.8711-1.9071	0.2997	142	0.3022	2691	X-RAY DIFFRACTION	98
1.9071-1.946	0.3588	142	0.3009	2694	X-RAY DIFFRACTION	98
1.946-1.9883	0.3283	140	0.2828	2662	X-RAY DIFFRACTION	98
1.9883-2.0346	0.3202	142	0.2613	2711	X-RAY DIFFRACTION	99
2.0346-2.0855	0.2753	143	0.2372	2703	X-RAY DIFFRACTION	98
2.0855-2.1419	0.2458	141	0.2282	2681	X-RAY DIFFRACTION	99
2.1419-2.2049	0.2023	142	0.2152	2693	X-RAY DIFFRACTION	99
2.2049-2.276	0.2276	141	0.2007	2690	X-RAY DIFFRACTION	99
2.276-2.3574	0.2278	144	0.2004	2727	X-RAY DIFFRACTION	99
2.3574-2.4518	0.2307	142	0.1913	2701	X-RAY DIFFRACTION	98
2.4518-2.5633	0.2312	141	0.1966	2691	X-RAY DIFFRACTION	98
2.5633-2.6985	0.2127	134	0.192	2536	X-RAY DIFFRACTION	93
2.6985-2.8675	0.2297	143	0.1944	2727	X-RAY DIFFRACTION	100
2.8675-3.0889	0.2083	145	0.1932	2746	X-RAY DIFFRACTION	100
3.0889-3.3996	0.2237	145	0.181	2749	X-RAY DIFFRACTION	99
3.3996-3.8912	0.2225	143	0.168	2727	X-RAY DIFFRACTION	99
3.8912-4.9015	0.1445	142	0.1508	2699	X-RAY DIFFRACTION	97
4.9015-43.5388	0.1941	142	0.1888	2697	X-RAY DIFFRACTION	97

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	1.3602	-0.091	0.5189	1.8414	0.8311	1.3518	0.1001	-0.1141	-0.3345	0.0613	-0.1449	-0.1641	0.4023	0.3187	0.0001	0.4267	0.0149	0.0057	0.4378	0.0162	0.5217	2.0993	44.6102	35.4769
2	1.1864	-0.6119	0.6133	0.7789	0.0979	0.5865	0.0512	0.3345	-0.4909	-0.5603	-0.3622	0.1457	0.7772	0.0191	0.0002	0.5045	0.0074	0.001	0.4608	-0.0033	0.576	-1.4889	39.1558	32.7881
3	2.306	-0.391	0.9485	2.3278	-0.1449	0.468	0.7313	0.5146	-0.8669	-1.3203	-0.4831	0.7265	0.8404	0.2203	0.0286	0.6267	0.0507	-0.1135	0.4281	-0.0906	0.6144	-2.7584	37.0068	26.1474
4	1.1084	-1.2056	-0.0389	1.8308	0.1578	0.3283	0.5128	1.1858	0.2824	-1.4118	-0.2505	-0.9594	-0.0981	0.5685	-0.0006	0.9235	0.0869	-0.1017	0.7152	-0.0717	0.5967	-11.2217	50.8432	14.966
5	0.459	-0.4125	0.1428	0.7109	-0.4773	0.4281	-0.0021	-0.0278	-0.588	-0.1463	0.0427	0.6642	0.4086	-0.5502	0.0013	0.4753	-0.0514	-0.0554	0.558	-0.0353	0.9095	-18.8433	48.2217	31.112
6	0.7453	-0.8752	0.5102	1.568	-0.5819	1.2687	0.0055	0.337	-0.1852	-0.3164	-0.1654	-0.2436	0.1347	0.3045	0	0.3299	-0.0077	0.0172	0.4308	-0.032	0.3767	-4.1447	58.6012	26.1244
7	2.7856	-1.592	0.8792	3.4951	-0.6267	1.5598	-0.1156	-0.0561	-0.0201	0.0605	0.0431	-0.2725	-0.0555	0.0815	-0.0001	0.2408	-0.0037	-0.0053	0.3551	-0.0115	0.3065	-2.3072	61.7822	34.2134
8	2.5336	-1.0815	0.0709	3.502	-1.2979	2.2487	0.0115	0.0303	0.3629	0.1052	-0.009	-0.0444	-0.464	-0.0012	0.0001	0.3008	0.0242	-0.0036	0.3422	-0.0452	0.2426	-13.8262	79.6704	30.4706
9	0.5583	-0.8366	0.8983	1.081	-1.0453	1.5348	-0.1738	-0.0164	-0.4734	-0.1957	-0.0056	0.0719	0.0111	-0.116	0.0002	0.4885	0.0291	-0.0049	0.6286	0.0169	0.5047	-18.7133	78.7666	21.5793
10	1.6641	0.9619	0.042	2.7942	0.9438	1.7974	-0.1123	0.0609	0.3899	-0.2641	0.067	0.1834	-0.0866	0.1547	0.0002	0.6058	-0.0018	0.0655	0.4229	0.0114	0.5775	19.9597	107.2509	46.7693
11	1.5832	2.0838	-0.3791	6.1299	-0.6909	2.1705	0.2937	-0.1894	0.7335	0.232	-0.0622	1.022	-0.3718	-0.132	-0.0036	0.485	0.0307	0.1379	0.4515	-0.0469	0.6628	11.3992	101.662	54.7954
12	1.9813	2.157	-1.0984	6.1375	-0.6188	2.3021	0.0132	-0.0221	0.0863	-0.4495	0.0267	-0.0189	0.2052	-0.0976	0.0002	0.4152	-0.019	-0.0034	0.3724	-0.0131	0.2805	14.6926	83.9312	49.7229
13	0.8444	-0.461	-0.0818	1.0724	-0.1351	1.2198	0.3043	0.0698	-0.8183	0.0835	0.0248	-0.6745	1.419	0.2675	0.0258	0.8114	-0.113	0.0184	0.5836	0.0052	0.548	9.3604	61.1	53.6232
14	1.5224	0.1281	1.3351	3.0913	-1.2616	2.3088	0.1633	-0.0205	-0.5259	-0.6225	0.0605	0.3888	0.3285	-0.3648	-0.0006	0.6433	-0.1261	-0.1176	0.4369	0.0383	0.47	6.3536	67.0339	51.8246

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 47 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 66 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 67 through 93 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 94 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 129 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 130 through 152 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 153 through 220 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 221 through 295 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 296 through 313 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 13 through 66 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 67 through 152 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 153 through 247 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 248 through 271 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 272 through 307 )

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