PDB-8jzt: The sigF and anti-sigma factor complex

ID or keywords:

Entry

Database: PDB / ID: 8jzt

Title

The sigF and anti-sigma factor complex

Components

Anti-sigma-F factor RsbW
RNA polymerase sigma factor SigF

Keywords

TRANSCRIPTION / SigF-usfx complex

Function / homology

Function and homology information

response to anoxia / RNA polymerase core enzyme binding / sigma factor antagonist activity / cellular response to nitrogen starvation / cellular response to cold / sigma factor activity / response to cold / DNA-templated transcription initiation / lipid metabolic process / response to oxidative stress ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

Chen, Y.J. / Su, D.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structure of SigF-usfx complex at 1.94 angstrom resolution
Authors: Chen, Y.J. / Su, D.

History

Deposition	Jul 6, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 16, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jzt.cif.gz	251.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8jzt.ent.gz	204.7 KB	Display	PDB format
PDBx/mmJSON format	8jzt.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/jz/8jzt ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jzt	HTTPS FTP

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Related structure data

Similar structure data	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	#48 - Dec 2003 Catabolite Activator Protein similarity (10)

Deposited unit

A: RNA polymerase sigma factor SigF

B: Anti-sigma-F factor RsbW

C: RNA polymerase sigma factor SigF

D: Anti-sigma-F factor RsbW

E: RNA polymerase sigma factor SigF

F: Anti-sigma-F factor RsbW

69.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA polymerase sigma factor SigF

B: Anti-sigma-F factor RsbW

A: RNA polymerase sigma factor SigF

B: Anti-sigma-F factor RsbW

defined by author&software
Evidence: cross-linking, DLS
46.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: RNA polymerase sigma factor SigF

D: Anti-sigma-F factor RsbW

E: RNA polymerase sigma factor SigF

F: Anti-sigma-F factor RsbW

defined by author&software
46.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.531, 79.550, 77.598
Angle α, β, γ (deg.)	90.00, 91.93, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	RNA polymerase sigma factor SigF / Sigma factor SigF / Alternative RNA polymerase sigma factor SigF / RNA polymerase sigma-F factor / ...Sigma factor SigF / Alternative RNA polymerase sigma factor SigF / RNA polymerase sigma-F factor / Sigma-F factor / Stress response/stationary phase sigma factor SigF Mass: 7983.212 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: sigF, Rv3286c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGI3
#2: Protein	Anti-sigma-F factor RsbW / Anti-sigma-F factor UsfX / Regulator of SigF / Sigma-F anti-sigma factor RsbW Mass: 15257.263 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: rsbW, usfX, Rv3287c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGX7
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.72 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5 and 23% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.94→77.55 Å / Num. obs: 60193 / % possible obs: 100 % / Redundancy: 11.4 % / R_merge(I) obs: 0.072 / Net I/σ(I): 19.4
Reflection shell	Resolution: 1.94→2.05 Å / R_merge(I) obs: 0.497 / Num. unique obs: 8747

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.94→38.78 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2094	2002	3.33 %
R_work	0.1692	-	-
obs	0.1705	60173	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.94→38.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4509	0	0	458	4967

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	0.978
X-RAY DIFFRACTION	f_dihedral_angle_d	4.99	654
X-RAY DIFFRACTION	f_chiral_restr	0.063	774
X-RAY DIFFRACTION	f_plane_restr	0.013	825

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 (%)
1.94-1.99	0.2622	152	0.2109	4115	X-RAY DIFFRACTION	100
1.99-2.05	0.2313	139	0.1778	4151	X-RAY DIFFRACTION	100
2.05-2.11	0.2516	140	0.1721	4147	X-RAY DIFFRACTION	100
2.11-2.18	0.1796	145	0.1644	4135	X-RAY DIFFRACTION	100
2.18-2.25	0.2176	141	0.1829	4094	X-RAY DIFFRACTION	100
2.25-2.34	0.2569	136	0.1838	4154	X-RAY DIFFRACTION	100
2.34-2.45	0.2276	144	0.1779	4153	X-RAY DIFFRACTION	100
2.45-2.58	0.234	139	0.178	4138	X-RAY DIFFRACTION	100
2.58-2.74	0.2358	150	0.1856	4155	X-RAY DIFFRACTION	100
2.74-2.95	0.2367	140	0.1815	4161	X-RAY DIFFRACTION	100
2.95-3.25	0.1892	147	0.1736	4166	X-RAY DIFFRACTION	100
3.25-3.72	0.2165	147	0.1584	4172	X-RAY DIFFRACTION	100
3.72-4.68	0.1746	143	0.1451	4165	X-RAY DIFFRACTION	100
4.68-10	0.1975	139	0.1723	4265	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	7.6524	2.8433	2.5344	7.5769	-3.5747	8.4574	0.3347	-0.7409	0.3239	0.9116	0.9444	1.4045	0.682	-1.2908	-1.4118	0.5971	-0.1041	-0.0241	1.1302	0.103	0.9293	35.1087	20.8534	11.9874
2	4.5986	0.7241	2.0748	4.198	0.1262	4.9773	0.0641	-0.3985	-0.08	-0.1141	-0.0969	0.7379	0.4625	-0.7313	-0.0331	0.4731	-0.0627	0.051	0.4281	0.0029	0.4194	45.7964	16.8837	16.2427
3	3.1427	1.2994	0.2434	4.2114	2.0881	2.532	0.382	-0.0532	-0.4195	-0.4453	-0.3832	-0.2943	1.2913	0.2445	0.0765	0.6717	0.0477	0.0521	0.3146	0.0463	0.3099	53.2794	11.06	16.4141
4	4.6713	-1.8194	2.8887	6.7132	-3.234	5.6451	0.2776	0.5153	0.3353	-0.8654	-0.5394	-0.009	0.707	0.2298	0.298	0.5925	-0.0631	-0.021	0.4116	-0.006	0.3177	47.5119	20.6365	6.8809
5	4.7473	0.743	0.8631	1.8188	0.6933	1.8013	-0.1672	-0.1425	-0.2099	0.0939	0.1528	-0.0172	-0.09	-0.0129	0.0113	0.2449	0.0068	0.0194	0.3057	0.0078	0.2282	63.2045	33.0418	2.2086
6	2.9948	0.9107	-3.9146	0.316	-1.0403	5.7499	0.0437	-0.6316	-0.3482	0.3592	-0.2089	-0.1817	-0.2535	0.0705	-0.0344	1.2864	-0.2502	-0.1854	1.1396	0.7201	1.2275	69.0119	24.4541	13.8871
7	4.2006	0.3167	-0.7203	2.7879	-0.8261	3.8074	-0.1281	-0.2551	-0.1763	0.1507	-0.0199	-0.1147	0.1564	0.0123	0.1059	0.2439	0.0475	0.0284	0.2581	-0.0007	0.2139	58.1731	34.1413	7.5969
8	3.2702	-0.5598	-0.9096	5.536	0.4692	3.4584	0.1309	-0.011	0.0976	-0.0433	-0.2393	0.1748	0.1556	0.2233	0.0945	0.2144	0.0168	0.0322	0.2504	-0.0219	0.2198	51.8171	40.6664	12.2141
9	0.4633	0.6641	0.8162	1.3199	1.4281	1.6163	0.2534	0.6201	-1.3507	-0.0727	0.149	0.2763	0.0984	0.0223	-0.6562	1.5573	-0.1803	-0.3124	1.2727	-0.5099	1.4103	30.1182	43.7411	7.0539
10	7.9236	0.3026	0.1432	0.728	-1.5964	5.8883	0.1045	0.3373	-1.1963	0.3125	0.4008	0.8857	0.1485	-0.9849	-0.6233	0.6642	-0.2051	0.1289	0.5774	0.2124	0.9993	20.8568	44.9907	13.8087
11	3.8605	-0.3994	0.3992	5.0561	-1.0811	3.4877	-0.113	0.2397	-0.6048	-0.2868	0.2954	0.7182	0.5759	-0.7335	-0.1158	0.3427	0.0289	-0.0409	0.3838	-0.0153	0.4377	21.9864	56.4465	7.8397
12	6.7548	-1.715	-0.6542	3.7699	-1.2861	3.0835	-0.0747	-0.0448	-0.0107	0.0026	0.2612	0.1492	-0.0683	0.0902	-0.0995	0.296	0.0774	-0.0882	0.3474	-0.0169	0.3746	19.3136	65.4707	6.2562
13	5.555	-2.7591	1.6478	6.2473	-2.8951	5.2472	-0.931	-0.8834	-0.1058	1.1729	0.8984	0.2235	-0.5428	-0.8274	-0.0043	0.4034	0.1041	0.0098	0.4979	-0.028	0.3238	24.5772	58.039	18.0143
14	3.6494	-3.5795	-4.3079	7.4953	7.1936	7.3055	-0.3395	0.5491	-0.4275	-0.711	-0.0835	-1.2637	0.0487	0.958	0.1084	0.4851	-0.0244	0.0989	0.4555	0.0065	0.5115	52.5769	71.0388	14.3291
15	3.185	0.9127	0.8914	3.345	1.4027	2.0629	-0.1434	0.1178	0.3275	-0.0712	-0.1177	0.4744	-0.4818	-0.0717	0.176	0.2818	-0.0245	-0.0163	0.2815	-0.0091	0.3475	39.3187	66.2043	23.1963
16	3.1049	0.2912	1.6266	3.3335	-0.8994	6.2639	-0.2034	0.0971	0.2262	-0.1029	-0.0565	0.1379	-0.2618	-0.0982	0.1816	0.2331	-0.0026	-0.0313	0.201	-0.0428	0.2375	40.9682	60.7912	18.0547
17	2.7688	-0.3861	0.1352	3.2716	1.0631	3.0445	-0.1252	0.1127	-0.1126	0.0237	-0.0053	-0.0521	-0.1083	0.201	0.0976	0.227	0.0015	-0.0298	0.2243	-0.0425	0.2473	44.4936	51.7604	14.2096
18	2.0049	-0.893	-0.5483	0.4271	0.2023	0.2061	0.3492	0.0372	-0.3325	-0.0576	0.6352	-0.1324	-0.1978	0.2047	-0.8701	1.3214	-0.0013	0.0362	1.8628	-0.5873	1.2012	50.9605	103.7397	49.2543
19	0.1725	-0.3224	-1.0593	0.8723	2.6201	8.2042	0.9563	-0.9163	-0.6189	1.3025	-0.4842	-1.0883	0.169	0.0426	-0.3692	0.8313	-0.0233	-0.2629	0.97	-0.2174	0.9184	60.1664	96.2313	44.9772
20	2.9867	0.2224	-1.454	3.9652	-0.9481	3.6808	0.1345	-0.3046	1.0363	0.1387	0.1113	-0.2266	-0.7773	0.1427	-0.1526	0.3563	-0.0045	0.0403	0.3002	-0.0589	0.4665	49.8221	100.8959	40.0562
21	4.0046	-0.1707	-2.127	3.7096	0.5349	3.6836	0.1048	-0.0358	0.149	-0.0197	0.0163	0.2805	-0.1761	-0.2314	-0.089	0.2371	0.0269	-0.0014	0.2651	0.0201	0.2899	42.5097	94.5001	38.8245
22	5.4036	-0.5887	0.3942	6.5781	-0.0153	9.7881	-0.1184	0.238	-1.1409	1.1896	-0.1279	-1.2055	0.6018	1.2969	-0.0331	0.5644	0.0103	-0.0564	0.461	0.0645	0.6353	49.7483	62.2106	36.7504
23	1.8212	0.3006	0.8344	2.8151	0.9618	1.8147	-0.0647	-0.0457	-0.0414	0.0428	0.0238	0.1933	0.1381	-0.1224	0.0299	0.2243	-0.0199	0.0065	0.2168	-0.0012	0.2184	51.8611	78.0865	34.6512

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 204 through 214 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 215 through 230 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 231 through 241 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 242 through 260 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 41 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 42 through 46 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 47 through 92 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 93 through 140 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 197 through 202 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 203 through 214 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 215 through 230 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 231 through 241 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 242 through 260 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 10 through 17 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 18 through 46 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 47 through 92 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 93 through 139 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 193 through 196 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 197 through 202 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 203 through 226 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 227 through 261 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 8 through 17 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 18 through 140 )

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