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- PDB-8hb3: Crystal structure of NAD-II riboswitch (two strands) with NR -

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Basic information

Entry
Database: PDB / ID: 8hb3
TitleCrystal structure of NAD-II riboswitch (two strands) with NR
Components
  • RNA (31-MER)
  • RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3')
KeywordsRNA / Riboswitch / NAD / NMN / Aptamer
Function / homologyNicotinamide riboside / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsPeng, X. / Lilley, D.M.J. / Huang, L.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
Cancer Research UKA18604 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets.
Authors: Peng, X. / Liao, W. / Lin, X. / Lilley, D.M.J. / Huang, L.
History
DepositionOct 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3')
B: RNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3494
Polymers17,8392
Non-polymers5102
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-14 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.982, 82.982, 65.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: RNA chain RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3')


Mass: 7802.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#2: RNA chain RNA (31-MER)


Mass: 10036.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus parasanguinis (bacteria)
#3: Chemical ChemComp-NNR / Nicotinamide riboside / 3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium


Mass: 255.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N2O5 / Feature type: SUBJECT OF INVESTIGATION
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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.87→65.63 Å / Num. obs: 6227 / % possible obs: 100 % / Observed criterion σ(I): 2.7 / Redundancy: 19 % / Biso Wilson estimate: 86.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.015 / Net I/σ(I): 23.2
Reflection shellResolution: 2.87→2.95 Å / Redundancy: 19.9 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 448 / CC1/2: 0.848 / Rpim(I) all: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HB1

8hb1


Resolution: 2.87→29.84 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 298 4.82 %
Rwork0.2005 5890 -
obs0.2011 6188 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.45 Å2
Refinement stepCycle: LAST / Resolution: 2.87→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1179 36 0 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051359
X-RAY DIFFRACTIONf_angle_d1.56772113
X-RAY DIFFRACTIONf_chiral_restr0.0504280
X-RAY DIFFRACTIONf_plane_restr0.006959
X-RAY DIFFRACTIONf_dihedral_angle_d18.1272649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.610.30781410.27142894X-RAY DIFFRACTION99.51
3.62-29.840.18171570.17912996X-RAY DIFFRACTION99.78
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)
12.547118055370.8230871879543.433492286524.76112666732-0.2519486187774.370998953890.276511491832-0.538896079288-0.366825770765-0.91200888587-0.1612681404440.6091986186440.459415296024-0.86176246962-0.314132127120.655690344154-0.187024284095-0.1604397906041.12469177909-0.0478075142550.78445986323-2.52976392306-33.502477032812.9963676333
22.894822824713.083973503330.4121633242513.59484035299-0.8550235467297.872149594170.08524990635210.9935167148990.55555140194-0.5929512461140.137746545083-0.101461281405-0.0227167994886-0.676743147788-0.07134834464840.798403088075-0.003529082832420.1012345386351.243734128180.1267645600760.7266194605419.3936859645-25.90364761524.30518225123
38.334102009721.745461599110.5290947811187.178222134353.75535827212.059211057252.03237487838-1.70050764446-0.8715625289520.304715903933-1.752003085292.11828591588-1.14694032318-0.691074317671-0.5706082476091.27230920565-0.01605368880830.156246114211.931621747470.387737925641.306463421533.16663338748-22.2284610706-6.28377930949
47.06981086093-1.92199110483-1.881609073132.12416960546-0.4810466584723.04550430439-0.263197296896-0.467967445737-0.4823541059110.112620005460.0183685266770.5350307849870.496393594482-2.622594499450.03012446046460.758427033463-0.3158925322550.05806267677622.00199910136-0.1360304638230.767142806849-9.5639464389-36.432773686211.8600491585
55.19972454175-0.4814798352061.248755843794.48825026920.4178189243565.13326089158-0.174467677343-0.6269529584750.0725075696132-0.0314682578781-0.2491307090351.125714853740.0411521785377-0.5068159288160.3780564875740.572536185299-0.19707388950.02390624759281.03677472108-0.1313964577480.6992427751873.63163699534-33.966206382215.150423481
68.999546642150.700009476675-1.918448884264.29483514705-4.201765544484.287863193530.673837247419-0.5819646736450.4834767425831.229987244420.435298993573-0.769214655659-0.1816954546080.0151425980833-0.02110081727412.28550319131-1.18731676005-0.1316672680513.143728218680.211364268241.9388821613128.1865681049-26.477260392816.629767505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 24 )AA11 - 24
3X-RAY DIFFRACTION3chain 'B' and (resid 26 through 30 )BB26 - 30
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 40 )BB31 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 55 )BB41 - 55
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 56 )BB56

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