PDB-8syk: Crystal structure of RNA device 43 truncation mutant 3 (U100C), h...

ID or keywords:

Entry

Database: PDB / ID: 8syk

Title

Crystal structure of RNA device 43 truncation mutant 3 (U100C), holo state

Components

RNA device 43 truncation mutant 3 (U100C)

Keywords

RNA / RNA device / aptazyme / tetracycline riboswitch / ribozyme

Function / homology

GUANOSINE-5'-TRIPHOSPHATE / TETRACYCLINE / RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.06 Å

Authors

Stagno, J.R. / Deme, J.C. / Lee, Y.-T. / Wang, Y.-X. / Lee, H.K. / Lea, S.M.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of RNA device 43 truncation mutant, holo state
Authors: Stagno, J.R. / Deme, J.C. / Lee, Y.-T. / Wang, Y.-X. / Lee, H.K. / Lea, S.M.

History

Deposition	May 25, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8syk.cif.gz	501 KB	Display	PDBx/mmCIF format
PDB format	pdb8syk.ent.gz	413.3 KB	Display	PDB format
PDBx/mmJSON format	8syk.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/sy/8syk ftp://data.pdbj.org/pub/pdb/validation_reports/sy/8syk	HTTPS FTP

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Related structure data

Related structure data	8t5o 8tkj 8tkk
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (3) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #65 - May 2005 Self-splicing RNA similarity (3) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (3)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (3)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#245 - May 2020
Spliceosomes
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: RNA device 43 truncation mutant 3 (U100C)

B: RNA device 43 truncation mutant 3 (U100C)

C: RNA device 43 truncation mutant 3 (U100C)

D: RNA device 43 truncation mutant 3 (U100C)

hetero molecules

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

1

A: RNA device 43 truncation mutant 3 (U100C)

hetero molecules

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

2

B: RNA device 43 truncation mutant 3 (U100C)

hetero molecules

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

3

C: RNA device 43 truncation mutant 3 (U100C)

hetero molecules

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

4

D: RNA device 43 truncation mutant 3 (U100C)

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.223, 81.223, 528.831
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: RNA chain	RNA device 43 truncation mutant 3 (U100C) Mass: 34516.688 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical	ChemComp-TAC / TETRACYCLINE Mass: 444.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₂H₂₄N₂O₈ / Comment: medication, antibiotic*YM
#4: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 3.69 Å³/Da / Density % sol: 66.67 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.05 M HEPES pH 7.5, 0.01 M MgCl2, 2.5 mM Spermine, 14% MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 3.06→528.84 Å / Num. obs: 35158 / % possible obs: 100 % / Redundancy: 12.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.029 / R_rim(I) all: 0.095 / Χ²: 0.98 / Net I/σ(I): 10.8 / Num. measured all: 427293
Reflection shell	Resolution: 3.06→3.21 Å / % possible obs: 100 % / Redundancy: 12.8 % / R_merge(I) obs: 2.148 / Num. measured all: 58097 / Num. unique obs: 4553 / CC_1/2: 0.464 / R_pim(I) all: 0.625 / R_rim(I) all: 2.239 / Χ²: 0.95 / Net I/σ(I) obs: 1.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.06→44.32 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2573	1770	5.06 %
R_work	0.2249	-	-
obs	0.2266	35012	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 168.2 Å²

Refinement step

Cycle: LAST / Resolution: 3.06→44.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	9392	61	21	9474

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Weight
X-RAY DIFFRACTION	f_bond_d	0.001	10509	0.085
X-RAY DIFFRACTION	f_angle_d	0.48	16386	0.217
X-RAY DIFFRACTION	f_dihedral_angle_d	15.175	5233
X-RAY DIFFRACTION	f_chiral_restr	0.025	2175
X-RAY DIFFRACTION	f_plane_restr	0.002	463

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 (%)
3.06-3.14	0.4074	125	0.3745	2491	X-RAY DIFFRACTION	100
3.14-3.24	0.337	125	0.2884	2511	X-RAY DIFFRACTION	100
3.24-3.34	0.2883	104	0.2891	2509	X-RAY DIFFRACTION	100
3.34-3.46	0.2661	126	0.2675	2498	X-RAY DIFFRACTION	100
3.46-3.6	0.3104	119	0.2618	2534	X-RAY DIFFRACTION	100
3.6-3.76	0.2936	137	0.2386	2500	X-RAY DIFFRACTION	100
3.76-3.96	0.2571	144	0.2394	2521	X-RAY DIFFRACTION	100
3.96-4.21	0.2932	145	0.2347	2519	X-RAY DIFFRACTION	100
4.21-4.53	0.2684	171	0.2456	2528	X-RAY DIFFRACTION	100
4.53-4.99	0.2629	138	0.2279	2551	X-RAY DIFFRACTION	100
4.99-5.71	0.2414	149	0.2248	2591	X-RAY DIFFRACTION	100
5.71-7.19	0.2948	139	0.2428	2646	X-RAY DIFFRACTION	100
7.19-44.32	0.2239	148	0.1887	2843	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	0.2487	0.0855	-0.289	0.0544	-0.4236	0.4135	-0.3979	-0.3226	-0.4957	-0.5415	0.1537	-0.0964	0.7571	-0.3575	0.3473	1.1395	-0.1635	-0.3283	1.7314	0.2497	0.9031	49.8543	-38.0765	24.1518
2	2.1433	0.7786	1.5616	0.0615	0.4422	0.5787	0.7467	0.0797	-1.0726	0.351	-0	-0.4742	0.6049	0.2286	-0.461	1.2812	-0.3425	-0.3594	2.0409	0.3586	1.0871	34.5422	-47.9497	20.9748
3	4.0661	-1.2588	3.6349	3.6069	-0.9879	3.2957	0.7483	-0.9621	0.6725	-0.0976	2.2141	-0.6001	-1.7349	-0.8016	-0.8809	1.4442	-0.3831	0.2611	1.8576	-0.3454	0.9955	1.5602	-43.8287	13.5829
4	3.8313	-0.8504	-1.7584	2.5065	0.4438	1.4663	-0.5743	-0.193	-1.7415	0.2701	-0.9114	1.3977	0.8278	-0.0403	0.8898	1.7248	-0.5906	-0.0938	1.6231	0.3393	1.6404	-1.6797	-66.5756	11.4983
5	5.3599	1.2271	1.9567	1.3144	0.4561	1.2802	0.2274	-0.6261	-1.3504	0.6669	0.8581	-0.5838	0.5346	-0.919	-0.8091	1.2282	-0.3407	-0.3392	2.1189	0.3706	1.2259	31.8095	-46.6881	12.7209
6	2.6708	-0.8657	0.8874	1.2891	-0.9803	0.9406	-1.2171	-0.5791	-0.6515	-0.7345	0.1145	-1.5042	-0.7574	0.271	0.5697	1.0377	0.0399	-0.1268	1.2431	0.3031	1.1564	63.9858	-34.9489	35.2178
7	0.3738	-0.5203	0.2542	3.2936	-0.5179	0.9871	-1.064	-0.9789	-0.1943	-0.418	0.2633	0.1042	-0.2955	0.2663	0.1796	0.6331	-0.5563	0.4735	1.7888	0.217	1.9262	62.9492	-7.2374	31.6111
8	3.1579	1.5557	-0.1685	0.7785	-0.0768	0.0077	-0.9262	-0.1851	-0.4442	0.1133	0.4749	0.4181	0.5778	-0.5304	0.0483	1.8767	-0.7033	0.3312	2.1347	0.0564	2.844	57.9144	-22.4617	55.2472
9	4.8793	-0.2028	-0.9173	2.1827	-0.8321	4.0537	-0.7885	-0.5849	0.094	-1.1164	0.7132	0.9658	1.5846	-0.6639	-0.42	1.271	-0.3884	-0.101	1.5747	0.5148	2.5635	51.6318	-14.219	38.048
10	3.4142	-2.0818	-3.3052	5.519	3.3433	4.0653	-0.0529	-1.6827	0.7246	-0.8208	0.9763	-1.9508	-1.609	1.8101	1.0862	1.2273	-0.2299	0.5272	2.5471	1.1324	1.9489	26.9243	-41.5069	52.8654
11	2.4516	0.9564	1.3584	2.0324	1.9567	2.1086	-0.5105	-1.9878	-0.0528	-0.1889	-0.3163	-0.7555	0.0587	1.6157	0.4388	0.7796	0.0255	0.0145	2.7925	0.5541	1.4386	10.3319	-37.23	56.1562
12	0.8244	-0.4126	-0.1275	3.075	-0.0941	1.2878	0.3364	-0.5373	1.6761	-0.8229	-0.5912	-0.4259	1.6973	-0.863	-0.4244	1.0342	-1.1774	0.1638	1.8011	0.3244	1.8254	63.3035	-9.8253	43.185
13	0.2045	0.1322	-0.5166	1.2469	-0.5122	0.5314	-0.4336	-0.1056	1.1241	0.107	0.3741	-0.7064	-0.1004	-0.0902	-0.1045	1.0902	-0.4519	-0.1502	1.1253	0.6551	1.8786	3.981	-24.4733	21.3663
14	4.0241	1.7341	-0.7743	3.9376	-1.5467	3.5749	0.4665	-0.2231	0.9923	-0.2625	-0.3377	-1.4498	-0.1032	0.7897	-0.3136	1.5893	-0.2079	0.2312	1.0358	0.3569	1.517	12.5349	-26.8863	27.5086
15	1.0539	1.6474	-0.8616	1.755	-0.781	0.4414	0.5872	-0.287	0.4583	0.5048	-0.5617	0.4041	-0.6231	0.8233	-0.1564	1.5858	-0.4868	-0.3617	1.3195	0.4312	1.6469	32.0845	-5.5868	14.2924
16	0.835	-0.0486	0.2978	0.9008	0.1054	2.1526	-0.8286	0.2389	-0.9079	0.112	-1.1644	0.0809	-0.4988	0.5292	-2.5861	2.1111	-0.5557	-1.2607	2.2687	1.7868	0.4189	48.633	4.2783	9.3956
17	1.6274	-0.8051	0.066	1.5286	0.2996	-0.3723	-0.9561	-0.0622	0.6297	-0.6733	0.3934	0.2583	-0.1306	0.2265	0.5097	1.5028	-0.3644	-0.2267	1.0939	0.2958	1.7222	36.7659	3.2832	20.1
18	1.2415	1.5613	-1.2398	2.6002	-2.6059	2.9616	0.345	0.1799	0.8137	-0.6824	0.5179	0.0643	-0.4913	-0.1054	-0.1647	1.9601	-0.5904	0.2706	1.1573	0.9183	0.2966	-3.4679	-41.8585	29.9982
19	4.2173	0.0306	0.2543	2.8803	0.3351	2.4251	-0.0914	-1.0734	-0.3425	-0.794	-0.3705	-1.7927	-0.2755	1.0863	0.4596	1.0637	-0.0763	-0.2348	1.212	0.3122	1.9549	1.0241	-72.1412	36.9179
20	1.7216	0.4235	0.4	0.2697	0.3976	0.7997	-0.8223	-0.7973	0.1657	0.0166	0.0952	0.5081	-0.3107	-0.0917	0.226	2.1999	-0.3678	-0.562	2.1982	0.9362	2.8717	19.2631	-79.9763	54.0476
21	4.6874	-1.3833	0.882	0.7252	-0.9561	2.0486	-2.9411	-0.1334	0.0105	0.3594	0.4116	-1.3585	-1.1396	1.0268	1.5618	1.5976	-0.2313	-0.1041	1.757	0.4482	3.0706	18.5927	-71.7525	42.8157
22	0.5796	-0.9411	0.07	8.1485	1.8189	0.9426	-0.6435	-0.4122	0.105	-0.6211	0.4326	2.5948	0.1267	0.3815	-1.2317	1.1004	0.0673	-0.4741	2.3491	1.1773	1.3867	54.5656	-60.9392	60.466
23	1.3753	0.0089	-0.6456	0.1042	-0.3672	0.703	-0.817	-0.9755	-0.442	-0.8185	1.2478	1.0674	1.155	-0.0301	-0.0191	1.0155	-0.6474	0.2214	1.4795	1.2316	2.1342	72.7707	-58.0154	45.5197
24	3.0464	-0.6946	0.3086	-0.0222	-0.4397	-0.0668	-0.8447	0.0913	-2.5151	-0.4999	-0.0705	-0.4215	0.071	0.6901	-1.6861	0.7982	0.452	-0.1264	1.5092	0.8554	2.7808	22.3126	-76.1987	48.4478

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and (resid 201 or resid 9:30))
2	X-RAY DIFFRACTION	2	(chain A and resid 31:54)
3	X-RAY DIFFRACTION	3	(chain A and resid 55:63)
4	X-RAY DIFFRACTION	4	(chain A and resid 64:92)
5	X-RAY DIFFRACTION	5	(chain A and resid 93:108)
6	X-RAY DIFFRACTION	6	(chain A and resid 109:115)
7	X-RAY DIFFRACTION	7	(chain B and (resid 201 or resid 9:16))
8	X-RAY DIFFRACTION	8	(chain B and resid 17:28)
9	X-RAY DIFFRACTION	9	(chain B and resid 29:42)
10	X-RAY DIFFRACTION	10	(chain B and resid 43:71)
11	X-RAY DIFFRACTION	11	(chain B and resid 72:102)
12	X-RAY DIFFRACTION	12	(chain B and resid 103:115)
13	X-RAY DIFFRACTION	13	(chain C and (resid 201 or resid 9:27))
14	X-RAY DIFFRACTION	14	(chain C and resid 28:37)
15	X-RAY DIFFRACTION	15	(chain C and resid 38:61)
16	X-RAY DIFFRACTION	16	(chain C and resid 62:75)
17	X-RAY DIFFRACTION	17	(chain C and resid 76:110)
18	X-RAY DIFFRACTION	18	(chain C and resid 111:115)
19	X-RAY DIFFRACTION	19	(chain D and (resid 201 or resid 9:16))
20	X-RAY DIFFRACTION	20	(chain D and resid 17:31)
21	X-RAY DIFFRACTION	21	(chain D and resid 32:46)
22	X-RAY DIFFRACTION	22	(chain D and resid 47:75)
23	X-RAY DIFFRACTION	23	(chain D and resid 76:92)
24	X-RAY DIFFRACTION	24	(chain D and resid 93:115)

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