PDB-4rzd: Crystal Structure of a PreQ1 Riboswitch

ID or keywords:

Entry

Database: PDB / ID: 4rzd

Title

Crystal Structure of a PreQ1 Riboswitch

Components

PreQ1-III Riboswitch (Class 3)

Keywords

RNA / Three-way Helical Junction / HL(OUT)-TYPE PSEUDOKNOT / Translational Regulation

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 /

SIRAS / Resolution: 2.75 Å

Authors

Wedekind, J.E. / Liberman, J.A. / Salim, M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.
Authors: Liberman, J.A. / Suddala, K.C. / Aytenfisu, A. / Chan, D. / Belashov, I.A. / Salim, M. / Mathews, D.H. / Spitale, R.C. / Walter, N.G. / Wedekind, J.E.

History

Deposition	Dec 20, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rzd.cif.gz	146.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4rzd.ent.gz	120.7 KB	Display	PDB format
PDBx/mmJSON format	4rzd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4rzd_validation.pdf.gz	420.9 KB	Display	wwPDB validaton report
Full document	4rzd_full_validation.pdf.gz	421.9 KB	Display
Data in XML	4rzd_validation.xml.gz	5.1 KB	Display
Data in CIF	4rzd_validation.cif.gz	6.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rz/4rzd ftp://data.pdbj.org/pub/pdb/validation_reports/rz/4rzd	HTTPS FTP

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Related structure data

Similar structure data	6axj-3 3fk3-d 6axj-1 6axj-4 6axj-2 3sb5-1 Search similar-shape structures by Omokage search (details) 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 (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) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #10 - Oct 2000 Ribosome similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (2) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #98 - Feb 2008 Small Interfering RNA similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #161 - May 2013 Ricin similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #227 - Nov 2018 Telomerase similarity (2) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #106 - Oct 2008 Poly(A) Polymerase 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 (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)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#245 - May 2020
Spliceosomes
similarity (2)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
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: PreQ1-III Riboswitch (Class 3)

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&software

Unit cell

Length a, b, c (Å)	84.083, 84.083, 278.365
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: RNA chain	PreQ1-III Riboswitch (Class 3) Mass: 32639.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.35 Å³/Da / Density % sol: 71.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 85% Tacsimate pH 7.0, 0.010 M Mg(C2H3O2)2, 0.006 M Co(NH3)6Cl3, and 0.001 M spermine HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.1696
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2010 / Details: RH COATED FOCUSING MIRROR
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1696 Å / Relative weight: 1
Reflection	Resolution: 2.75→46.4 Å / Num. obs: 25223 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / R_merge(I) obs: 0.034 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.75→2.85 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 79.3

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

SIRAS / Resolution: 2.75→38.294 Å / SU ML: 0.46 / Isotropic thermal model: isotropic with TLS / σ(F): 1.33 / Phase error: 29.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2277	2526	10.01 %
R_work	0.2121	-	-
obs	0.2138	25223	88.15 %

Solvent computation

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

Displacement parameters

B_iso mean: 122 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→38.294 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	2116	13	4	2133

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2383
X-RAY DIFFRACTION	f_angle_d	0.554	3704
X-RAY DIFFRACTION	f_dihedral_angle_d	15.736	1186
X-RAY DIFFRACTION	f_chiral_restr	0.024	494
X-RAY DIFFRACTION	f_plane_restr	0.002	100

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 (%)
2.7502-2.8031	0.5861	101	0.4743	875	X-RAY DIFFRACTION	60
2.8031-2.8603	0.5079	109	0.4552	1025	X-RAY DIFFRACTION	74
2.8603-2.9224	0.3585	142	0.4067	1223	X-RAY DIFFRACTION	85
2.9224-2.9904	0.3736	143	0.3613	1288	X-RAY DIFFRACTION	90
2.9904-3.0651	0.3218	140	0.3216	1200	X-RAY DIFFRACTION	85
3.0651-3.148	0.3137	127	0.307	1367	X-RAY DIFFRACTION	93
3.148-3.2406	0.3346	157	0.2695	1372	X-RAY DIFFRACTION	94
3.2406-3.3451	0.3034	147	0.2535	1301	X-RAY DIFFRACTION	93
3.3451-3.4646	0.2624	152	0.2465	1351	X-RAY DIFFRACTION	94
3.4646-3.6032	0.1761	139	0.2193	1302	X-RAY DIFFRACTION	91
3.6032-3.7671	0.2176	139	0.1853	1213	X-RAY DIFFRACTION	85
3.7671-3.9655	0.1946	156	0.1776	1374	X-RAY DIFFRACTION	96
3.9655-4.2136	0.1951	143	0.1675	1362	X-RAY DIFFRACTION	95
4.2136-4.5385	0.1696	149	0.1541	1313	X-RAY DIFFRACTION	92
4.5385-4.9943	0.251	135	0.1799	1238	X-RAY DIFFRACTION	86
4.9943-5.715	0.1762	159	0.1704	1353	X-RAY DIFFRACTION	95
5.715-7.1925	0.1824	142	0.1927	1277	X-RAY DIFFRACTION	89
7.1925-38.2978	0.2153	146	0.1993	1263	X-RAY DIFFRACTION	89

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	9.8585	5.8749	3.6358	5.1039	1.4699	1.6014	0.0726	-0.2896	1.7375	0.3699	0.6023	1.8278	-0.3242	-1.7053	-0.6506	1.9962	0.2537	0.2441	1.244	0.1415	0.4875	37.1079	39.2845	123.296
2	5.0869	-0.7803	-2.2149	4.0699	-1.3178	3.2352	-0.0137	-0.7008	-1.4981	0.0148	0.5575	-1.1467	-0.9794	0.6054	0.4974	1.3629	0.2264	-0.0573	0.8636	0.0483	0.0639	39.3866	28.9558	107.6021
3	4.0429	0.1615	-4.754	4.2963	-0.0654	5.8469	1.1965	-0.4682	0.5163	0.1025	-0.2009	0.1079	0.9554	0.3938	-1.0838	1.3244	0.0761	-0.0834	1.0738	0.0721	0.4122	41.5035	36.6475	99.7705
4	1.5848	-0.0694	2.1429	9.6044	-2.6027	7.8719	-0.1484	-0.2372	-0.0725	-0.9976	0.4102	0.4395	0.5882	-0.118	-0.3667	0.9908	0.1191	0.0378	0.8835	-0.0044	0.3905	33.523	33.329	113.7477
5	7.2643	-5.2236	-4.5057	5.1327	4.6968	4.4109	0.8581	0.2204	0.9062	-0.478	0.0401	-0.5287	-0.7227	-0.7228	-0.8498	1.2859	0.0648	0.1518	0.9334	-0.143	0.4813	38.617	31.0438	127.894
6	2.1182	-3.5345	1.7214	6.345	-3.7675	2.9436	-0.4864	-2.7558	0.1866	0.2431	2.251	0.2475	0.513	0.0335	-1.8183	1.6741	0.1749	0.2523	1.651	-0.0452	0.7768	27.0777	37.0813	138.2514
7	9.1976	-7.1088	9.1756	2.0018	-6.2372	9.2889	2.4933	-0.1372	-0.9713	0.3683	1.6748	2.3521	1.0587	0.7088	-3.3768	1.8711	0.0528	-0.0679	2.9373	0.5015	1.204	27.8178	25.0148	148.1332
8	2.2044	2.6377	-1.6162	3.695	-2.7496	2.5652	2.2184	1.2947	0.2225	0.8013	-1.2439	2.5724	-1.6212	-0.3939	-0.7622	2.8272	0.2254	0.386	2.1839	-0.069	1.6393	29.5826	30.8837	155.9265
9	1.9814	4.729	6.2753	4.9546	4.7864	5.4303	-1.7542	-1.1255	-0.488	-2.1836	-0.4763	1.0371	-0.6017	-2.7687	2.3623	1.6108	0.2018	0.0482	2.0861	-0.137	0.7456	33.9241	26.5048	142.0879
10	6.2434	-5.5453	0.9434	6.0806	0.015	5.2782	0.5131	1.3123	-0.6868	-0.2367	0.943	1.0839	-0.6461	1.658	-1.4248	1.537	0.0489	0.0675	1.4963	0.227	0.7123	24.3302	32.7553	131.2186
11	0.9973	2.0279	-2.0995	4.3662	-5.0353	6.1497	-0.147	-1.6646	-1.0778	1.3443	-0.6108	1.3185	-1.1279	0.2939	0.6257	1.2381	0.4415	0.2089	1.3541	0.362	0.8944	24.3276	38.9796	112.2155
12	1.2654	1.2285	-2.1713	8.8151	0.1457	3.7343	0.1623	0.4149	-0.1375	1.1034	-0.3908	0.6887	-0.3276	0.1248	0.2017	0.9472	0.1904	-0.1596	0.8347	-0.0736	0.5484	9.1253	48.2741	107.4996
13	6.0228	2.5864	-1.4929	1.3749	-0.4154	1.598	-1.1104	-1.1235	1.0721	-0.7115	0.5309	0.6391	-0.2148	-0.1016	0.5561	1.2849	0.3358	-0.0765	1.1061	0.0228	0.6832	1.4455	64.5836	102.4823
14	8.6938	0.5115	5.1294	4.6067	0.1272	3.0197	0.0757	0.8823	-0.257	0.1171	0.2389	0.4888	0.3098	0.8155	-0.1678	1.0105	0.1139	-0.0469	0.9692	0.0937	0.5149	7.0433	53.7053	100.1202
15	3.1535	-1.0258	3.5285	5.9172	0.9861	5.0126	0.317	-0.241	-1.0694	0.2542	0.7241	0.6812	0.5599	-0.2306	-0.7039	1.1648	0.1982	0.0718	0.8663	-0.0164	0.5527	14.3729	44.436	115.4991
16	8.1293	-2.0352	-1.1577	6.3005	-1.2392	1.8113	0.4515	-0.4918	-0.8839	1.0835	-0.8422	-0.9557	-0.5131	0.0596	0.5391	1.1007	0.0804	0.0747	0.8014	0.0513	1.0174	13.196	33.3122	109.1728
17	8.6653	5.5562	-4.7607	8.1155	-0.7227	8.4181	1.0173	-0.4894	-0.2187	0.6811	-0.6714	0.2832	-0.0988	0.7573	-0.3914	0.9855	0.2566	-0.0428	0.8407	0.1105	0.5048	30.0723	36.8036	103.6932
18	3.1478	3.5928	-0.106	4.3597	1.0474	6.6517	0.5326	0.117	0.3397	0.6029	0.4876	-0.2337	-0.288	-0.7042	-1.0625	1.3702	0.0294	-0.0343	1.0277	0.0395	0.5111	43.6209	43.2932	93.3331
19	3.6295	-0.7236	-3.5117	0.2939	0.5054	3.3883	-1.3769	-1.3598	-1.0728	0.8467	1.1784	-0.4169	-0.5665	1.6525	0.3677	1.28	0.1198	-0.1598	1.535	0.3006	0.8069	53.3199	28.4798	93.3761
20	3.1415	-3.0503	2.813	4.1572	-1.847	3.345	-1.0576	-0.5783	-0.4294	0.4516	0.1675	-0.8167	-1.266	1.4929	1.2363	1.4695	-0.0268	-0.2148	1.8484	0.3387	1.8102	69.0956	26.4555	91.0341

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:4)
2	X-RAY DIFFRACTION	2	(chain A and resid 5:9)
3	X-RAY DIFFRACTION	3	(chain A and resid 10:14)
4	X-RAY DIFFRACTION	4	(chain A and resid 15:20)
5	X-RAY DIFFRACTION	5	(chain A and resid 21:24)
6	X-RAY DIFFRACTION	6	(chain A and resid 25:28)
7	X-RAY DIFFRACTION	7	(chain A and resid 29:32)
8	X-RAY DIFFRACTION	8	(chain A and resid 33:41)
9	X-RAY DIFFRACTION	9	(chain A and resid 42:45)
10	X-RAY DIFFRACTION	10	(chain A and resid 46:49)
11	X-RAY DIFFRACTION	11	(chain A and resid 50:54)
12	X-RAY DIFFRACTION	12	(chain A and resid 55:62)
13	X-RAY DIFFRACTION	13	(chain A and resid 63:68)
14	X-RAY DIFFRACTION	14	(chain A and resid 69:75)
15	X-RAY DIFFRACTION	15	(chain A and resid 76:79)
16	X-RAY DIFFRACTION	16	(chain A and resid 80:83)
17	X-RAY DIFFRACTION	17	(chain A and resid 84:88)
18	X-RAY DIFFRACTION	18	(chain A and resid 89:92)
19	X-RAY DIFFRACTION	19	(chain A and resid 93:96)
20	X-RAY DIFFRACTION	20	(chain A and resid 97:101)

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