PDB-8dh3: T7 RNA polymerase elongation complex with unnatural base dPa

ID or keywords:

Entry

Database: PDB / ID: 8dh3

Title

T7 RNA polymerase elongation complex with unnatural base dPa

Components

Non-template strand DNA
RNA
T7 RNA polymerase
Template strand DNA

Keywords

Transferase/DNA/RNA / T7 RNA polymerase / elongation complex / unnatural base / Ds-Pa / synthetic DNA / transcription / Transferase-DNA-RNA complex

Function / homology

Function and homology information

DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Escherichia phage T7 (virus)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Model details

T7 RNA polymerase, elongation complex, unnatural base pair, synthetic DNA

Authors

Oh, J. / Wang, D.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Authors: Oh, J. / Kimoto, M. / Xu, H. / Chong, J. / Hirao, I. / Wang, D.

History

Deposition	Jun 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8dh3.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb8dh3.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	8dh3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8dh3_validation.pdf.gz	574.1 KB	Display	wwPDB validaton report
Full document	8dh3_full_validation.pdf.gz	629.2 KB	Display
Data in XML	8dh3_validation.xml.gz	113.7 KB	Display
Data in CIF	8dh3_validation.cif.gz	155.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/8dh3 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/8dh3	HTTPS FTP

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Related structure data

Related structure data	8dh0SC 8dh1C 8dh2C 8dh4C 8dh5C S: Starting model for refinement C: citing same article (ref.)
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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

B: T7 RNA polymerase

A: Template strand DNA

C: RNA

D: Non-template strand DNA

E: T7 RNA polymerase

F: Template strand DNA

G: RNA

H: Non-template strand DNA

I: T7 RNA polymerase

J: Template strand DNA

K: RNA

L: Non-template strand DNA

M: T7 RNA polymerase

N: Template strand DNA

O: RNA

P: Non-template strand DNA

444 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: T7 RNA polymerase

A: Template strand DNA

C: RNA

D: Non-template strand DNA

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

2

E: T7 RNA polymerase

F: Template strand DNA

G: RNA

H: Non-template strand DNA

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

3

I: T7 RNA polymerase

J: Template strand DNA

K: RNA

L: Non-template strand DNA

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

4

M: T7 RNA polymerase

N: Template strand DNA

O: RNA

P: Non-template strand DNA

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

Unit cell

Length a, b, c (Å)	79.067, 86.271, 201.967
Angle α, β, γ (deg.)	89.700, 86.010, 69.450
Int Tables number	1
Space group name H-M	P1

#1: Protein	T7 RNA polymerase / DNA-directed RNA polymerase Mass: 98984.227 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P00573, DNA-directed RNA polymerase
#2: DNA chain	Template strand DNA Mass: 5510.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain	RNA Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	Non-template strand DNA Mass: 2666.761 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.55 % / Mosaicity: 0.24 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2021

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.93→47.98 Å / Num. obs: 105382 / % possible obs: 98.4 % / Redundancy: 3.5 % / B_iso Wilson estimate: 90.68 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.114 / R_pim(I) all: 0.071 / R_rim(I) all: 0.134 / Net I/σ(I): 5.9 / Num. measured all: 371631

Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.93-2.98	2.204	19142	5176	0.306	1.33	2.58	0.4	98.1
16.05-47.98	0.026	2296	615	0.999	0.016	0.03	28.1	94

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.4	data scaling
PHENIX	1.19	refinement
PDB_EXTRACT	3.27	data extraction
PHENIX	1.19	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8DH0

8dh0

Resolution: 3→47.98 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2755	1850	1.88 %
R_work	0.2471	96319	-
obs	0.2477	98169	98.35 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 416.21 Å² / B_iso mean: 136.6622 Å² / B_iso min: 33.99 Å²

Refinement step

Cycle: final / Resolution: 3→47.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25642	2656	0	0	28298
Num. residues	-	-	-	-	3416

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3-3.08	0.4058	134	0.383	7395	7529	97
3.08-3.17	0.3757	146	0.3373	7386	7532	98
3.17-3.27	0.3603	128	0.3239	7376	7504	98
3.27-3.39	0.3595	159	0.3191	7395	7554	98
3.39-3.53	0.2934	131	0.2986	7424	7555	98
3.53-3.69	0.3209	153	0.2675	7393	7546	98
3.69-3.88	0.321	137	0.2478	7437	7574	98
3.88-4.12	0.2597	136	0.2519	7473	7609	98
4.12-4.44	0.2703	153	0.2203	7335	7488	98
4.44-4.89	0.2378	138	0.2115	7450	7588	99
4.89-5.6	0.2446	148	0.2329	7439	7587	99
5.6-7.05	0.2792	142	0.2637	7424	7566	99
7.05-47.98	0.2363	145	0.2076	7392	7537	98

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	1.9905	0.449	0.2379	0.2676	-0.6454	2.1728	0.4975	1.8552	0.8778	-0.0878	-0.4575	-0.1763	0.0682	0.5452	0.1161	0.8335	0.2032	0.1525	1.251	0.4897	1.1834	37.4258	54.375	-54.9644
2	2.3534	0.5392	-0.0863	0.5843	-0.1505	1.2079	-0.0317	0.9992	0.6979	-0.0983	-0.0244	-0.1577	-0.1525	0.2781	0.0103	0.71	0.0099	-0.0023	0.8957	0.3053	0.9022	25.9491	52.1147	-48.9371
3	2.4175	-0.3958	0.0281	1.1827	-0.0959	1.2604	0.0408	0.4476	-0.0512	-0.0914	-0.0708	-0.0366	0.125	0.0271	0.0277	0.4219	-0.0469	0.0703	0.4038	-0.0646	0.4671	18.5541	28.1975	-35.5654
4	2.0835	1.8468	-0.961	1.7538	-1.6541	4.7388	0.2488	0.9306	-0.0559	-0.2029	0.0064	-1.7281	0.1912	1.7453	-0.3109	0.6395	0.0846	-0.0737	1.3727	-0.1381	1.4688	35.5357	34.4336	-45.9155
5	5.515	5.1956	-3.5265	5.0722	-3.0207	5.6339	0.5825	2.3189	0.6373	-0.9059	-0.5961	-0.1136	0.0988	0.7131	-0.0813	0.7314	0.1305	0.0406	1.1979	0.257	0.8957	27.4453	43.4363	-41.3462
6	0.0076	-0.0089	-0.0122	0.0004	0.0041	0.0068	0.1457	0.7246	-0.0253	-1.4926	-0.7984	0.2269	0.4175	-0.2305	0.5771	3.3546	0.8495	-0.6803	1.9121	0.0024	2.4373	43.5964	20.8623	-47.5303
7	2.0291	0.7031	0.2726	2.4119	0.354	1.1041	0.1019	-1.1199	-1.182	0.4903	-0.0108	-0.9122	0.6308	0.2329	-0.1755	0.8586	0.1245	-0.0196	1.4248	0.3223	1.3867	35.454	55.2691	9.2898
8	2.8612	0.3259	-0.4027	1.7438	-0.056	1.0328	0.0618	-1.0466	-0.287	-0.0341	-0.2723	-0.1584	-0.0689	0.1798	0.1572	0.5531	0.1187	0.0478	0.7236	-0.1361	0.572	36.3538	82.1632	-5.3271
9	4.4971	-2.6294	-0.4695	1.572	0.3415	0.0959	1.1749	-0.5268	1.3986	-0.7986	-0.5806	-1.3363	0.124	1.1954	-0.4976	1.2002	0.0102	-0.1337	2.0103	0.2045	1.9025	61.0923	73.5481	1.4319
10	6.1514	1.6141	0.1715	1.8352	1.4662	5.9577	-0.3233	-0.7259	-1.4045	-0.8735	-0.1957	-0.3369	0.8691	0.6756	0.6575	1.1547	-0.0173	0.1306	1.3195	0.4708	1.4473	32.6525	61.3905	3.6914
11	3.4246	0.3435	0.3392	5.8687	-0.165	5.2044	0.4851	-1.3708	-0.566	0.0056	0.1841	-0.9485	0.598	1.209	-0.4828	0.9653	0.0406	-0.0391	1.4958	0.1159	1.188	36.3205	64.8964	-1.795
12	2.2147	1.2405	-0.9716	2.4966	1.9442	3.8702	-1.1473	0.2489	0.6668	0.127	-0.9934	-0.4716	0.0865	-0.3621	1.6367	2.1517	0.5969	0.0799	2.8205	0.0225	3.159	65.3631	74.8836	2.7074
13	2.9263	-1.0398	-0.2829	1.516	-0.2428	1.886	-0.0183	0.2483	0.9517	0.0159	0.0146	0.1565	-0.6002	-0.2706	-0.0494	0.8386	-0.1429	-0.0131	0.759	0.0275	1.1204	0.0309	45.195	-95.3838
14	3.0901	-0.31	0.6429	2.113	-0.0957	2.9492	0.3199	-0.2884	-0.4132	-0.2917	0.1348	0.4854	0.9492	-0.4228	-0.3293	1.1204	-0.3679	-0.3325	0.8944	0.1274	0.7357	9.8759	9.3826	-91.3829
15	-0.0003	0.0657	0.0423	1.3468	0.8079	0.4839	0.6955	-0.195	0.5631	0.8014	-0.1502	1.3376	0.0981	-2.021	-0.5128	1.0771	-0.4865	-0.0179	2.5655	0.5596	1.637	-5.9056	22.6714	-88.6737
16	7.3422	-1.44	1.1146	2.7283	-2.339	5.8007	0.4638	-0.1484	0.7503	-0.6046	0.4145	2.1759	0.3508	-1.4433	-0.844	0.9716	-0.2237	-0.1566	1.3652	0.208	1.5088	4.1803	22.1688	-98.1809
17	1.3112	-0.3478	0.6648	0.3282	-0.68	1.4142	-0.9755	-0.0277	0.0519	0.2168	-1.0755	0.3279	-0.1522	-0.2989	1.3623	3.3188	-0.6422	-0.3667	2.9175	0.182	3.537	-17.4188	16.1066	-78.1861
18	3.3306	1.6723	0.3288	2.5282	-0.6951	2.1131	0.3042	0.9052	-1.5484	-0.7304	-0.2023	-0.0798	0.7222	0.6767	-0.3852	1.9266	0.3298	-0.6035	1.5689	-0.2865	1.4954	24.9869	-14.1063	51.6061
19	2.2136	1.3472	0.1273	1.2283	-0.4445	1.1496	0.4953	-0.5672	0.0864	0.3926	-0.3612	0.4453	0.5997	-1.0654	-0.7408	1.4665	-0.165	-0.2399	2.202	0.6538	1.6397	-13.5975	-9.3367	62.8369
20	1.7238	-0.2218	1.4459	0.5093	-0.0789	1.2223	-0.0301	0.8753	-0.0689	-0.0336	-0.2621	0.1634	0.5149	0.7126	-0.3247	1.3776	0.2408	-0.1298	1.6834	-0.2395	0.7996	18.1397	-6.1216	42.6124
21	1.8955	-0.0882	1.6293	1.3217	-0.2363	2.8413	0.1967	0.4151	0.0506	0.2065	-0.3035	-0.4194	-0.1735	1.0617	0.1793	1.027	-0.2829	-0.0673	1.9053	0.1103	0.6695	31.0209	16.5291	57.8581
22	1.0533	-0.617	0.2004	1.0913	-0.8989	0.9245	-0.3013	-0.7735	0.8894	-0.2692	-0.777	-0.0767	-0.8689	-0.2918	0.5557	1.5289	0.0193	-0.2559	1.5805	-0.4537	0.949	4.5835	35.5042	58.8967
23	2.7545	0.0403	0.9069	0.9049	0.366	3.2576	-0.3836	0.8266	0.3207	-0.3601	-0.1594	0.0659	-0.7011	0.7893	0.3197	1.1839	-0.2343	-0.1754	1.6675	0.0988	0.6771	11.7471	21.7269	40.7748
24	3.0761	-2.998	-4.1605	2.9679	4.0572	5.6282	0.686	2.8703	-0.3045	-3.2693	-0.4301	1.1622	0.9663	-1.1863	-0.2604	4.3361	0.6641	-0.3596	4.1831	-0.8936	3.287	-21.2524	23.7284	43.2263
25	3.909	0.0243	-1.6813	3.2109	2.4405	3.2728	-0.1628	-0.3971	0.3471	0.9224	-0.3413	0.8616	-1.433	-0.1462	0.3687	1.7229	0.0653	0.1287	1.5443	-0.0064	1.0109	-0.4404	18.4411	50.216
26	0.7928	0.0626	1.3349	0.561	0.5625	2.6275	0.3752	-0.1619	-1.2579	1.7338	0.3106	1.386	-0.6656	0.17	-0.1254	1.5263	-0.3092	0.1917	1.9329	0.2086	1.0835	12.5464	2.3837	57.9541
27	1.8354	0.0289	1.9281	3.0511	1.1693	2.4524	0.9682	-0.7865	-0.3832	0.7152	-0.3213	1.5513	-0.3765	-0.3096	-0.2196	1.2919	-0.1757	0.0567	2.0648	-0.2375	1.0154	10.7568	9.5005	58.8557
28	2.161	1.2537	-0.8643	3.7431	-1.0919	0.4683	-0.5128	0.0899	-0.4841	0.1871	0.0423	-0.5018	0.0569	-0.5588	0.2517	3.7181	0.6714	0.0561	3.3601	0.1944	4.0406	-12.2762	23.5265	44.6146

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 193 )	B	1 - 193
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 194 through 407 )	B	194 - 407
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 408 through 883 )	B	408 - 883
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 3 through 18 )	A	3 - 18
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 0 through 8 )	C	0 - 8
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 2 through 8 )	D	2 - 8
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 4 through 407 )	E	4 - 407
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 408 through 883 )	E	408 - 883
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 2 through 12 )	F	2 - 12
10	X-RAY DIFFRACTION	10	chain 'F' and (resid 13 through 18 )	F	13 - 18
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 1 through 8 )	G	1 - 8
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 2 through 9 )	H	2 - 9
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 5 through 283 )	I	5 - 283
14	X-RAY DIFFRACTION	14	chain 'I' and (resid 284 through 883 )	I	284 - 883
15	X-RAY DIFFRACTION	15	chain 'J' and (resid 3 through 18 )	J	3 - 18
16	X-RAY DIFFRACTION	16	chain 'K' and (resid 1 through 8 )	K	1 - 8
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 2 through 8 )	L	2 - 8
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 2 through 61 )	M	2 - 61
19	X-RAY DIFFRACTION	19	chain 'M' and (resid 62 through 247 )	M	62 - 247
20	X-RAY DIFFRACTION	20	chain 'M' and (resid 248 through 313 )	M	248 - 313
21	X-RAY DIFFRACTION	21	chain 'M' and (resid 314 through 569 )	M	314 - 569
22	X-RAY DIFFRACTION	22	chain 'M' and (resid 570 through 653 )	M	570 - 653
23	X-RAY DIFFRACTION	23	chain 'M' and (resid 654 through 882 )	M	654 - 882
24	X-RAY DIFFRACTION	24	chain 'N' and (resid 2 through 6 )	N	2 - 6
25	X-RAY DIFFRACTION	25	chain 'N' and (resid 7 through 12 )	N	7 - 12
26	X-RAY DIFFRACTION	26	chain 'N' and (resid 13 through 18 )	N	13 - 18
27	X-RAY DIFFRACTION	27	chain 'O' and (resid 1 through 8 )	O	1 - 8
28	X-RAY DIFFRACTION	28	chain 'P' and (resid 2 through 9 )	P	2 - 9

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