8TNS | pdb_00008tns

Solution structure of poly(UG) RNA (GU)12 G-quadruplex


SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion1
Scattering Typex-ray
Radiation/Neutron SourceADVANCE PHOTON SOURCE
SynchrotronY
Beamline TypeAPS
Detector TypePILATUS 2M AND PILATUS 300K
Detector Manufacturer Details
Temperature (K)295
pH7
Numer of Time Frames Used60
Protein Concentration Range (mg/mL)0.26-1.6
Sample BufferHEPES
Data Reduction SoftwareIN-HOUSE SOFTWARE
Guiner Mean Radius Of Gyration (nm)1.3
Sigma Mean Radius Of Gyration0.007
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)4.7
Solution Scattering Data Analysis and Model Fitting
MethodSoftwareSoftware AuthorsStarting ModelConformers, Number CalculatedConformers, Number SubmittedConformers, Selection CriteriaBest Representative ConformerOther Details
HIGH TEMPERATURE DYNAMICS AT 3000 K, FOLLOWED BY SUMULATED ANNEALING FROM 3000 K TO 25 K AND A FINAL ENERGY MINIMIZATION STEP.X-PLOR_NIHSCHWIETERS, KUSZEWSKI, TJANDRA, CLORE10020LEAST RESTRAINT VIOLATIONS1STARTING MODEL WAS BEST MODEL OBTAINED AFTER CALCULATIONS WITHOUT RDC AND SCATTERING DATA.
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
11D 1H400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Bruker AVANCE III 600
21D 31P200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Bruker AVANCE III 600
33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
43D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced CC decoupled200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
52D H,H NOESY-1H,15N-HSQC200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
62D H,N HCN BEST200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
72D 1H-13C HSQC sensitivity-enhanced CC decoupled (H1'-C1' H5-C5)200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
82D 1H-15N HSQC long-range200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
92D 1H-13C HSQC sensitivity-enhanced CC decoupled (H6-C6)200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
102D 1H-15N HSQC BEST200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
113D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
123D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced CC decoupled200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
133D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced CC decoupled200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
143D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
153D HCCH-TOCSY200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
163D HCCH-COSY200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
172D 1H-13C HSQC constant-time200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
183D HCP sensitivity-enhanced200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III 600
193D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to ribose)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
203D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to H8-C8)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
212D H,H NOESY-1H,15N-HSQC350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 600
222D H,N HCN BEST350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 800
232D 1H-13C HSQC sensitivity-enhanced CC decoupled350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 800
242D 1H-15N HSQC long-range (H8-N9)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 800
252D 1H-13C HSQC sensitivity-enhanced350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 800
262D 1H-15N HSQC BEST350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 800
273D H,N,N NOESY-1H,15N-HSQC350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm276Varian VNMRS DD 800
282D 1H-15N HSQC BEST350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm276Varian VNMRS DD 800
292D 1H-13C HSQC sensitivity-enhanced350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm276Varian VNMRS DD 800
302D 1H-13C HSQC constant-time350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm276Varian VNMRS DD 800
313D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to Ribose)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
323D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to H8-C8)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
333D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to unlabeled H8-C8)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
343D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to unlabeled Ribose)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
353D HCCH-TOCSY350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
363D HCCH-COSY350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
372D 1H-13C HSQC constant-time350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
383D HCP sensitivity-enhanced350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III 600
392D 1H-1H NOESY (200 ms mix. time)400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III 600
402D 1H-1H NOESY (350 ms mix. time)400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III 600
412D 1H-1H TOCSY400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III 600
422D 1H-1H NOESY400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Bruker AVANCE III 600
432D 1H-1H NOESY500 uM (GU)11.5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
442D 1H-1H TOCSY500 uM (GU)11.5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
452D 1H-1H NOESY500 uM (GU)11.5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
462D 1H-1H TOCSY500 uM (GU)11.5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
472D 1H-1H NOESY350 uM (GU)12-dG1, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
482D 1H-1H TOCSY350 uM (GU)12-dG1, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
492D 1H-1H NOESY350 uM (GU)12-dG1, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
502D 1H-1H TOCSY350 uM (GU)12-dG1, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
512D 1H-1H NOESY770 uM (GU)12-dU2, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
522D 1H-1H TOCSY770 uM (GU)12-dU2, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
532D 1H-1H NOESY770 uM (GU)12-dU2, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
542D 1H-1H TOCSY770 uM (GU)12-dU2, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 600
552D 1H-1H NOESY380 uM (GU)12-dG3, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
562D 1H-1H TOCSY380 uM (GU)12-dG3, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 800
572D 1H-1H NOESY380 uM (GU)12-dG3, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
582D 1H-1H TOCSY380 uM (GU)12-dG3, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Varian VNMRS DD 800
592D 1H-1H NOESY270 uM (GU)12-dU4, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III HD 750
602D 1H-1H NOESY270 uM (GU)12-dU4, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Bruker AVANCE III HD 750
612D 1H-1H NOESY190 uM (GU)12-dG5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III HD 750
622D 1H-1H NOESY190 uM (GU)12-dG5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm276Bruker AVANCE III HD 750
632D 1H-1H NOESY210 uM (GU)12-dU6, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Bruker AVANCE III 600
642D 1H-13C HSQC sensitivity-enhanced CC decoupled350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
652D 1H-13C HSQC sensitivity-enhanced CC decoupled200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O100% D2O100 mM7.01 atm293Varian VNMRS DD 600
662D 1H-15N HSQC long-range (H8-N7)350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Varian VNMRS DD 800
672D 13C-15N CON (C2-N1)200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Bruker AVANCE III HD 750
682D 13C-15N CON (C2-N3)200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Bruker AVANCE III HD 750
692D 1H-13C HN(CA)CO (H3-C2)200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O90% H2O/10% D2O100 mM7.01 atm293Bruker AVANCE III HD 750
702D ARTSY120 uM [U-13C; U-15N]-Gua (GU)12, 21 mM potassium phosphate, 60 mM potassium chloride, 0.02 % sodium azide, 0.8 mM magnesium chloride, 20 mg/mL Pf1 phage, 50 % H2O, 50 % [U-2H] D2O50% H2O/50% D2O100 mM7.01 atm293Varian VNMRS DD 600
712D ARTSY70 uM [U-13C; U-15N]-Ura (GU)12, 21 mM potassium phosphate, 60 mM potassium chloride, 0.02 uM sodium azide, 0.8 uM magnesium chloride, 20 uM Pf1 phage, 50 % H2O, 50 % [U-2H] D2O50% H2O/50% D2O100 mM7.01 atm293Varian VNMRS DD 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III HD750
2BrukerAVANCE III600
3VarianVNMRS DD600
4VarianVNMRS DD800
NMR Refinement
MethodDetailsSoftware
simulated annealing, torsion angle dynamicsSAXS and RDC were used during refinementX-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number100
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionVnmrJ4.2 revision AAgilent
2collectionTopSpin3.5Bruker Biospin
3data analysisMestreLab (Mnova / MestReNova / MestReC)14.3.1-31739Mestrelab Research
4peak pickingNMRFAM-SPARKY1.470NMRFAM
5chemical shift assignmentNMRFAM-SPARKY1.470NMRFAM
6processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7structure calculationX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
8refinementX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore