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- PDB-8keb: Crystal structure of 2'-dG-III riboswitch with 2'-dG -

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Basic information

Entry
Database: PDB / ID: 8keb
TitleCrystal structure of 2'-dG-III riboswitch with 2'-dG
ComponentsRNA (72-MER)
KeywordsRNA / Riboswitch / 2'-Deoxyguanosine / 2'-dG / Aptamer
Function / homology2'-DEOXY-GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiao, W. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
Citation
Journal: Nucleic Acids Res. / Year: 2025
Title: Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family.
Authors: Chen, K. / Liao, W. / Wang, J. / Ren, Y. / Lu, Z. / Peng, X. / Wang, J. / Huang, L.
#1: Journal: Nucleic Acids Res. / Year: 2025
Title: A general strategy for engineering GU base pairs to facilitate RNA crystallization.
Authors: Ren, Y. / Lin, X. / Liao, W. / Peng, X. / Deng, J. / Zhang, Z. / Zhan, J. / Zhou, Y. / Westhof, E. / Lilley, D.M.J. / Wang, J. / Huang, L.
History
DepositionAug 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 10, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (72-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8876
Polymers23,0251
Non-polymers8625
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-11 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.516, 26.834, 65.227
Angle α, β, γ (deg.)90.000, 112.710, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (72-MER)


Mass: 23024.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus sp. (bacteria)

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Non-polymers , 5 types, 11 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


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

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.08 M Sodium chloride, 0.01 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 6.4, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine ...Details: 0.08 M Sodium chloride, 0.01 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 6.4, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride, 0.1M Glycine.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→64.35 Å / Num. obs: 11351 / % possible obs: 96.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 71.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.021 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.704 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1337 / CC1/2: 0.378 / Rpim(I) all: 1.103 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.43 Å / SU ML: 0.3836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.8279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 554 4.94 %
Rwork0.202 10669 -
obs0.2039 11223 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 54 6 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571733
X-RAY DIFFRACTIONf_angle_d1.09552694
X-RAY DIFFRACTIONf_chiral_restr0.0456362
X-RAY DIFFRACTIONf_plane_restr0.007373
X-RAY DIFFRACTIONf_dihedral_angle_d15.4638863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.53951140.45262419X-RAY DIFFRACTION87.07
2.42-2.770.39771630.37572690X-RAY DIFFRACTION99.13
2.77-3.490.26481250.25352724X-RAY DIFFRACTION97.04
3.49-34.430.19541520.14942836X-RAY DIFFRACTION98.22
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)
11.73378116412-0.5364574131861.458061351060.395012430477-0.6287271102441.506129345310.107875944298-0.3037558333280.2510194845420.2586156501490.216059378322-0.1345802931430.214168462318-0.639865564580.01004473246260.750868487258-0.02648223784180.04772070555930.524941478152-0.05146700429280.803876835354-28.1607722237-3.5278533133315.3938905002
20.617943730134-0.3655757347610.4090712025771.20481657869-0.1677708671710.502336859906-0.266926559287-2.299964880720.04238399021990.6799617773870.595206350230.0762610589296-0.699739601498-0.779622697807-0.06563444135340.895399937989-0.004469906231430.01012223327992.554927059160.3694116067270.88367739843-34.0592841757-8.5137614146440.8122675859
30.26026784849-0.04381164374630.0228118790720.07584175609470.01851727299850.1693748559010.388984861691-1.137617482940.4450056171360.1877171352180.2736862616590.1528989496330.192567329554-0.4912697261660.001617522774480.8702097110240.2082391795420.03518310142620.9576310988220.0680266321270.91968525676-41.42431668872.5781168318519.1354516998
44.51170097192-0.362991912471.823501455181.66877295335-0.4585360671070.5711474707260.11277578935-0.9819246803870.1350015325960.2836798214610.223814559439-0.2050078887930.235032431515-0.85067776306-0.003180139956660.6952790919070.0501622134672-0.004474248779020.580259834662-0.02432966924980.776780614197-24.9881968242-6.5875130910723.391221246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )AB2 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 31 )AB17 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 36 )AB32 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 72 )AB37 - 72

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