PDB-8toz: Class III PreQ1 riboswitch double mutant U8C/A85G

ID or keywords:

Entry

Database: PDB / ID: 8toz

Title

Class III PreQ1 riboswitch double mutant U8C/A85G

Components

Class-III preQ1 riboswitch

Keywords

RNA / PREQ1 / QUEUOSINE / THREE-WAY HELICAL JUNCTION / APTAMER / METABOLITE / TRANSLATIONAL REGULATION / HL(OUT)-TYPE PSEUDOKNOT / RIBOSWITCH

Function / homology

7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Faecalibacterium prausnitzii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 3 Å

Authors

Srivastava, Y. / Jenkins, J.L. / Wedekind, J.E.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2024
Title: Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.
Authors: Srivastava, Y. / Akinyemi, O. / Rohe, T.C. / Pritchett, E.M. / Baker, C.D. / Sharma, A. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.

History

Deposition	Aug 4, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details 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 / _citation.year / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8toz.cif.gz	141.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/to/8toz ftp://data.pdbj.org/pub/pdb/validation_reports/to/8toz	HTTPS FTP

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Related structure data

Related structure data	6xknC 6xkoC 8vpvC C: citing same article (ref.)
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 (2) #130 - Oct 2010 Riboswitches similarity (3) #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) #210 - Jun 2017 Adenine Riboswitch in Action similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #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) #65 - May 2005 Self-splicing RNA 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 (2)
#130 - Oct 2010
Riboswitches
similarity (3)
#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)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#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)
#65 - May 2005
Self-splicing RNA
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: Class-III preQ1 riboswitch

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	84.082, 84.082, 280.826
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: RNA chain	Class-III preQ1 riboswitch Mass: 32654.270 Da / Num. of mol.: 1 / Mutation: U8C, A85G / Source method: obtained synthetically / Source: (synth.) Faecalibacterium prausnitzii (bacteria)
#2: Chemical	ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₉N₅O / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.37 Å³/Da / Density % sol: 71.83 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 65% Tacsimate pH 7, 50mM Na-CacodylatepH 7, 1mM Spermine HCl, 0.006M Hexammine Cobalt (III)Chloride, 5mM Mg Acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 3→38.35 Å / Num. obs: 21799 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC_1/2: 0.976 / R_pim(I) all: 0.09 / Net I/σ(I): 6.5
Reflection shell	Resolution: 3→3.18 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1953 / CC_1/2: 0.961 / R_pim(I) all: 0.879 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 3→38.35 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2221	2163	9.92 %
R_work	0.2021	-	-
obs	0.2041	21797	98.07 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→38.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	2052	13	5	2070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2303
X-RAY DIFFRACTION	f_angle_d	0.694	3585
X-RAY DIFFRACTION	f_dihedral_angle_d	13.506	1158
X-RAY DIFFRACTION	f_chiral_restr	0.03	478
X-RAY DIFFRACTION	f_plane_restr	0.006	98

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 (%)
3-3.07	0.3909	132	0.3467	1268	X-RAY DIFFRACTION	96
3.07-3.15	0.3033	132	0.3426	1290	X-RAY DIFFRACTION	96
3.15-3.23	0.3367	148	0.2983	1316	X-RAY DIFFRACTION	96
3.23-3.33	0.2697	140	0.2684	1270	X-RAY DIFFRACTION	96
3.33-3.43	0.2619	144	0.2624	1271	X-RAY DIFFRACTION	97
3.43-3.56	0.269	137	0.2532	1304	X-RAY DIFFRACTION	96
3.56-3.7	0.2401	149	0.2209	1290	X-RAY DIFFRACTION	97
3.7-3.87	0.2367	146	0.1998	1307	X-RAY DIFFRACTION	98
3.87-4.07	0.2107	138	0.1842	1330	X-RAY DIFFRACTION	99
4.07-4.33	0.1738	143	0.169	1319	X-RAY DIFFRACTION	100
4.33-4.66	0.2087	151	0.163	1355	X-RAY DIFFRACTION	100
4.66-5.13	0.2057	148	0.1787	1313	X-RAY DIFFRACTION	100
5.13-5.87	0.1875	154	0.1744	1340	X-RAY DIFFRACTION	100
5.87-7.38	0.2077	145	0.1728	1333	X-RAY DIFFRACTION	100
7.38-38.35	0.2137	156	0.1939	1328	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	1.2992	-0.1641	0.4744	0.6611	-0.7004	3.061	-0.0347	0.1173	0.1569	-0.0795	0.2393	0.065	-0.3545	-0.0441	0.2624	1.4715	0.0973	-0.0139	1.2153	0.0568	0.1126	39.6306	32.5707	112.2689
2	0.0483	0.0739	-0.1158	0.1704	-0.1833	0.2612	-0.0536	0.0242	0.1142	0.0323	0.1414	0.1659	-0.1804	0.0529	0.6101	1.3153	0.1632	0.0096	1.4402	0.0316	0.0638	38.1328	34.0055	111.6188
3	4.533	-0.6618	-0.8138	2.5972	0.3817	1.8752	0.1768	-0.8309	-0.0624	0.5674	0.6403	0.3469	0.168	-0.1328	-0.1387	1.8146	0.1386	0.1838	1.702	0.0867	0.4489	29.3461	33.8066	139.4242
4	5.5602	-4.008	5.0131	2.9289	-3.614	4.5232	0.9675	-1.1389	1.4418	1.7222	1.2545	0.4273	-0.4817	-4.533	-2.2625	2.5578	0.3519	0.0648	2.7745	0.1941	1.5894	32.2857	28.7196	154.2597
5	6.2238	-4.2846	7.012	6.3956	-3.7177	8.2623	-0.2671	0.1621	0.2214	-0.1923	0.6229	-0.168	0.5797	0.0957	-0.286	1.6269	-0.028	0.0228	1.8725	0.0352	0.5436	29.5086	31.6703	135.9026
6	1.9014	0.2278	0.7432	2.8534	-0.1109	2.3628	-0.1135	-0.1824	0.0687	0.0183	-0.5731	0.0681	-1.1771	0.1506	0.5293	1.1835	0.3715	0.0106	1.5005	0.0184	0.4395	19.7436	39.823	105.9064
7	1.1318	0.6644	1.3218	1.6774	0.895	1.5505	0.1568	0.2426	-0.1251	0.1702	0.074	0.0463	0.1077	0.1704	-0.1681	1.3603	0.0992	-0.0317	1.2083	-0.0994	0.4165	8.1988	52.7133	109.2699
8	1.2148	0.3912	-0.1116	3.2722	0.5993	0.3381	-0.2082	0.1801	0.3017	0.5694	0.349	0.5809	0.0179	-0.3555	-0.0827	1.2764	0.1363	0.0044	1.1815	0.0621	0.445	0.3027	60.4335	101.6942
9	2.4697	0.6419	-2.4008	1.0422	1.0596	5.5739	-0.2048	-0.0143	-0.3365	0.1893	0.321	-0.2035	0.6978	0.5843	-0.1419	1.4221	0.2066	-0.0144	1.1944	-0.0002	0.2261	14.988	48.3393	111.1564
10	5.9885	-2.5917	1.9982	8.4466	-3.7625	1.8875	-0.437	-1.7978	-0.743	1.6757	0.6271	0.6501	-0.2316	0.7404	-0.2862	1.1219	0.1074	-0.0495	1.1529	0.0142	0.6192	15.6378	32.5842	109.4651
11	1.1884	0.4367	-1.6256	0.2336	-0.6143	2.2111	0.2034	0.1457	0.0772	-0.0061	0.1124	0.0099	-0.3945	0.3585	-0.075	1.4331	0.2038	0.0074	1.2719	-0.0684	0.1726	40.1165	39.4849	98.0523
12	8.2404	2.3299	-0.8221	5.3839	-0.5864	0.1083	-0.3734	-2.7207	-1.2371	0.4879	-0.3174	-1.1814	-0.5389	0.4909	0.6429	1.6267	0.1572	-0.1591	1.8411	0.2957	1.2754	65.8448	26.3191	92.302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 10 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 22 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 23 through 30 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 31 through 40 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 41 through 51 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 52 through 56 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 57 through 63 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 64 through 72 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 73 through 79 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 80 through 84 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 85 through 94 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 95 through 101 )

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