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- PDB-8fb3: PreQ1-1 (type-1) riboswitch with stacked metabolites and a C10-G3... -

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Basic information

Entry
Database: PDB / ID: 8fb3
TitlePreQ1-1 (type-1) riboswitch with stacked metabolites and a C10-G34 base pair in the expression platform
ComponentsRNA (34-MER) Riboswitch
KeywordsRNA / riboswitch / Shine-Dalgarno sequence / pseudoknot / A-amino kissing motif / quintuple-base transition motif
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciesCarnobacterium antarcticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWedekind, J.E. / Schroeder, G.M. / Jenkins, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM063162 United States
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: A riboswitch separated from its ribosome-binding site still regulates translation.
Authors: Schroeder, G.M. / Akinyemi, O. / Malik, J. / Focht, C.M. / Pritchett, E.M. / Baker, C.D. / McSally, J.P. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.
#1: Journal: Nat Commun / Year: 2022
Title: A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.
Authors: Schroeder, G.M. / Cavender, C.E. / Blau, M.E. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.
#2: Journal: Methods Mol Biol / Year: 2023
Title: Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model.
Authors: Cavender, C.E. / Schroeder, G.M. / Mathews, D.H. / Wedekind, J.E.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (34-MER) Riboswitch
B: RNA (34-MER) Riboswitch
C: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,70012
Polymers32,5523
Non-polymers1,1489
Water1086
1
A: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2585
Polymers10,8511
Non-polymers4074
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2093
Polymers10,8511
Non-polymers3582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2334
Polymers10,8511
Non-polymers3833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.867, 67.612, 50.589
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (34-MER) Riboswitch


Mass: 10850.541 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Carnobacterium antarcticum (bacteria)
#2: Chemical
ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.43 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.2 M ammonium acetate, 0.01 M magnesium acetate tetrahydrate, and 0.05 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2022
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→35.2 Å / Num. obs: 5588 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rpim(I) all: 0.051 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.2 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 871 / Rpim(I) all: 0.339 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
PHENIX(1.20.1_4487)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→35.16 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.75 / Stereochemistry target values: ML
Details: NCS restraints were applied throughout except for the last cycle of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 548 10 %random
Rwork0.2245 ---
obs0.2286 5478 97.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.8 Å2
Refinement stepCycle: LAST / Resolution: 3→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2071 3 6 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022309
X-RAY DIFFRACTIONf_angle_d0.7263576
X-RAY DIFFRACTIONf_dihedral_angle_d15.6851121
X-RAY DIFFRACTIONf_chiral_restr0.028469
X-RAY DIFFRACTIONf_plane_restr0.003100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.34421300.29061174X-RAY DIFFRACTION94
3.3-3.780.2861380.28251233X-RAY DIFFRACTION98
3.78-4.760.24911390.25911247X-RAY DIFFRACTION99
4.76-35.160.2531410.18181276X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
16.18031.9792-4.47134.8658-3.30464.0670.12410.01621.16281.9731-0.46271.8484-1.9469-0.02270.42741.3792-0.14250.43610.6008-0.03151.4234-19.3574-14.2561-17.1237
21.3827-1.7241.4082.4398-1.8321.46181.65820.14530.08243.1371-1.9859-0.4876-2.06681.2640.81061.1634-0.4495-0.07181.02880.17781.7697-7.1562-0.1712-20.1589
35.92843.35880.33683.9783-0.97825.71750.8656-0.5242.80251.82080.10451.7093-0.0634-1.3016-0.54031.76090.34270.11420.7728-0.0151.5901-16.14874.096-23.2131
47.7281-7.733.44062.05982.88027.52952.10621.47411.11862.8743-3.78291.6219-1.936-3.23660.95681.44970.04860.49981.6235-0.0471.4633-21.2354-7.7871-27.1958
59.4821-0.06373.08872.02672.54321.2994-0.00331.62070.36351.6983-0.3139-2.2036-0.913-0.6785-0.15590.8710.05530.24250.93030.30671.1738-11.0455-15.9547-21.4785
64.8525-3.5159-1.5892.03479.43032.113-0.6955-1.91180.1965.0087-1.21591.33470.45670.13371.88822.1739-0.4067-0.06141.24440.23771.4599-15.5908-18.8555-10.3692
72.15650.6531-4.162.0847-1.0582.02441.6035-1.80440.6481.0885-0.5119-2.0114-1.78411.8059-1.14681.0446-0.0758-0.1861.14650.11611.5474-4.0698-8.7381-19.775
82.03091.68922.03972.00642.02932.0268-0.7494-0.073-3.1617-1.13761.62152.5331-0.05540.2321-0.77631.11880.1851-0.01241.1821-0.2491.66019.09-7.9151-44.5662
92.1706-6.165-4.81259.9111-0.70992.1767-0.6124-2.1372-1.37870.01320.81570.2796-0.73860.88940.14521.05440.32960.02411.20620.00590.92525.54831.0027-31.8321
101.92152.8105-3.33265.5024-2.01617.1508-0.59250.76681.94080.6759-1.57481.8379-0.6206-2.09461.59340.79650.29510.13461.0183-0.20451.3516-4.0387.0909-32.9725
116.0387-2.15293.38652.03314.79527.58-0.56341.0020.83140.1062-0.78932.19032.3674-0.50040.77331.1512-0.03280.06550.8979-0.04581.3103-0.17880.8761-46.0604
128.0615-1.56970.98766.8589-1.212.06930.1665-0.03050.17730.05640.0227-0.85741.17062.2459-0.26451.0110.2028-0.06631.3338-0.11790.769713.4590.9385-41.1713
133.8644-3.7494-0.68712.03490.80126.77460.0407-1.88440.8919-0.3476-0.0659-2.43961.25142.164-0.19550.78860.4297-0.07061.9958-0.08581.176112.3281.6725-31.771
149.7887-2.9508-3.40612.1727-3.54968.19960.5479-0.18253.7469-0.7436-0.43890.009-0.9263-0.49830.46130.83140.0455-0.14780.9236-0.06051.346-0.176310.8983-40.4568
151.43980.76011.64524.5270.03521.94190.5202-0.873-0.2683-0.3497-0.5767-0.19970.41380.14730.44421.46890.48350.36931.3769-0.01591.075811.6546-6.4359-2.4741
162.45591.769-1.00164.39720.40192.9274-0.56541.71730.3688-3.04080.75471.4431-0.15480.457-0.48121.6925-0.191-0.27451.4227-0.0370.797617.58286.8209-14.5117
176.74053.8186-2.59432.0308-0.04954.52120.68940.8242-0.4307-0.2584-0.9273-2.3995-0.07931.33250.03270.9920.03640.00821.1878-0.1221.048227.19287.3038-10.0238
189.79742.78125.20446.42340.42969.36930.40770.3655-0.2557-0.43580.1603-0.69121.56540.0828-0.3351.13320.0544-0.00411.0155-0.12140.92616.41714.1544-0.7891
196.65530.25350.80669.3342-6.22975.6244-0.6497-1.12540.034-0.38852.29441.37852.5008-1.9737-1.66311.29070.0102-0.12621.3543-0.06920.79693.9683-3.6517-6.6284
209.41192.7032-1.82645.94951.97031.9837-0.2894-0.28280.6149-1.9849-2.8614-0.08224.21112.13722.35021.3510.1774-0.54982.5427-0.18120.9788.4569-2.5486-15.459
217.0103-0.47862.15735.30072.16688.235-0.20080.5854-0.8889-1.10750.37680.8572-2.02250.50620.04531.07110.033-0.21770.83990.24171.341519.105812.2662-6.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 9 )
3X-RAY DIFFRACTION3chain 'A' and (resid 10 through 13 )
4X-RAY DIFFRACTION4chain 'A' and (resid 14 through 17 )
5X-RAY DIFFRACTION5chain 'A' and (resid 18 through 21 )
6X-RAY DIFFRACTION6chain 'A' and (resid 22 through 26 )
7X-RAY DIFFRACTION7chain 'A' and (resid 27 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 4 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 8 )
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 12 )
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 16 )
12X-RAY DIFFRACTION12chain 'B' and (resid 17 through 21 )
13X-RAY DIFFRACTION13chain 'B' and (resid 22 through 30 )
14X-RAY DIFFRACTION14chain 'B' and (resid 31 through 34 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 4 )
16X-RAY DIFFRACTION16chain 'C' and (resid 5 through 9 )
17X-RAY DIFFRACTION17chain 'C' and (resid 10 through 13 )
18X-RAY DIFFRACTION18chain 'C' and (resid 14 through 19 )
19X-RAY DIFFRACTION19chain 'C' and (resid 20 through 24 )
20X-RAY DIFFRACTION20chain 'C' and (resid 25 through 28 )
21X-RAY DIFFRACTION21chain 'C' and (resid 29 through 34 )

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