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- PDB-8tns: Solution structure of poly(UG) RNA (GU)12 G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 8tns
TitleSolution structure of poly(UG) RNA (GU)12 G-quadruplex
ComponentsRNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*U)-3')
KeywordsRNA / G-quadruplex / p(UG)-fold
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing, torsion angle dynamics
AuthorsEscobar, C.A. / Petersen, R. / Butcher, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Solution Structure of Poly(UG) RNA.
Authors: Escobar, C.A. / Petersen, R.J. / Tonelli, M. / Fan, L. / Henzler-Wildman, K.A. / Butcher, S.E.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)7,7721
Polymers7,7721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*U)-3')


Mass: 7771.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic21D 1H
125isotropic21D 31P
135isotropic33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced
145isotropic33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced CC decoupled
155isotropic32D H,H NOESY-1H,15N-HSQC
165isotropic32D H,N HCN BEST
175isotropic32D 1H-13C HSQC sensitivity-enhanced CC decoupled (H1'-C1' H5-C5)
185isotropic32D 1H-15N HSQC long-range
195isotropic32D 1H-13C HSQC sensitivity-enhanced CC decoupled (H6-C6)
1105isotropic32D 1H-15N HSQC BEST
1116isotropic43D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced
1126isotropic43D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced CC decoupled
1136isotropic43D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced CC decoupled
1146isotropic33D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced
1156isotropic33D (H)CCH-TOCSY
1166isotropic33D (H)CCH-COSY
1176isotropic42D 1H-13C HSQC constant-time
1186isotropic23D HCP sensitivity-enhanced
1193isotropic33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to ribose)
1203isotropic33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to H8-C8)
1213isotropic32D H,H NOESY-1H,15N-HSQC
1223isotropic42D H,N HCN BEST
1233isotropic42D 1H-13C HSQC sensitivity-enhanced CC decoupled
1243isotropic42D 1H-15N HSQC long-range (H8-N9)
1253isotropic42D 1H-13C HSQC sensitivity-enhanced
1263isotropic42D 1H-15N HSQC BEST
2273isotropic43D H,N,N NOESY-1H,15N-HSQC
2283isotropic42D 1H-15N HSQC BEST
2293isotropic42D 1H-13C HSQC sensitivity-enhanced
2303isotropic42D 1H-13C HSQC constant-time
1314isotropic33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to Ribose)
1324isotropic33D H,H,C NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to H8-C8)
1334isotropic33D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to unlabeled H8-C8)
1344isotropic33D H,H,C 13C-filtered NOESY-1H,13C-HSQC sensitivity-enhanced (NOEs to unlabeled Ribose)
1354isotropic33D (H)CCH-TOCSY
1364isotropic33D (H)CCH-COSY
1374isotropic32D 1H-13C HSQC constant-time
1384isotropic23D HCP sensitivity-enhanced
1392isotropic22D 1H-1H NOESY (200 ms mix. time)
1402isotropic22D 1H-1H NOESY (350 ms mix. time)
1412isotropic22D 1H-1H TOCSY
1421isotropic22D 1H-1H NOESY
1437isotropic42D 1H-1H NOESY
1447isotropic42D 1H-1H TOCSY
2457isotropic42D 1H-1H NOESY
2467isotropic42D 1H-1H TOCSY
1478isotropic42D 1H-1H NOESY
1488isotropic42D 1H-1H TOCSY
2498isotropic42D 1H-1H NOESY
2508isotropic42D 1H-1H TOCSY
1519isotropic42D 1H-1H NOESY
1529isotropic42D 1H-1H TOCSY
2539isotropic42D 1H-1H NOESY
2549isotropic32D 1H-1H TOCSY
15510isotropic42D 1H-1H NOESY
15610isotropic42D 1H-1H TOCSY
25710isotropic42D 1H-1H NOESY
25810isotropic42D 1H-1H TOCSY
15911isotropic12D 1H-1H NOESY
26011isotropic12D 1H-1H NOESY
16112isotropic12D 1H-1H NOESY
26212isotropic12D 1H-1H NOESY
16313isotropic22D 1H-1H NOESY
1644isotropic32D 1H-13C HSQC sensitivity-enhanced CC decoupled
1656isotropic32D 1H-13C HSQC sensitivity-enhanced CC decoupled
1663isotropic42D 1H-15N HSQC long-range (H8-N7)
1675isotropic12D 13C-15N CON (C2-N1)
1685isotropic12D 13C-15N CON (C2-N3)
1695isotropic12D 1H-13C HN(CA)CO (H3-C2)
17014anisotropic32D ARTSY
17115anisotropic32D ARTSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O, 90% H2O/10% D2O(GU)12, H2O90% H2O/10% D2O
solution2400 uM (GU)12, 50 mM HEPES, 150 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2O(GU)12, D2O100% D2O
solution3350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O, 90% H2O/10% D2OG-(GU)12, H2O90% H2O/10% D2O13C-15N G labeled (GU)12 RNA
solution4350 uM [U-13C; U-15N]-Gua (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OG-(GU)12, D2O100% D2O13C-15N G labeled (GU)12 RNA
solution5200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 10 % [U-2H] D2O, 90 % H2O, 90% H2O/10% D2OU-(GU)12, H2O90% H2O/10% D2O13C-15N U labeled (GU)12 RNA
solution6200 uM [U-13C; U-15N]-Ura (GU)12, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OU-(GU)12, D2O100% D2O13C-15N U labeled (GU)12 RNA
solution7500 uM (GU)11.5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2O(GU)11.5100% D2Osequence GUGUGUGUGUGUGUGUGUGUGUG
solution8350 uM (GU)12-dG1, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OdG1100% D2O(GU)12 RNA with a deoxyribose substitution at position 1
solution9770 uM (GU)12-dU2, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OdU2100% D2O(GU)12 RNA with a deoxyribose substitution at position 2
solution10380 uM (GU)12-dG3, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OdG3100% D2O(GU)12 RNA with a deoxyribose substitution at position 3
solution11270 uM (GU)12-dU4, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OdU4100% D2O(GU)12 RNA with a deoxyribose substitution at position 4
solution12190 uM (GU)12-dG5, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OdG5100% D2O(GU)12 RNA with a deoxyribose substitution at position 5
solution13210 uM (GU)12-dU6, 20 mM potassium phosphate, 100 mM potassium chloride, 20 uM DSS, 100 % [U-2H] D2O, 100% D2OdU6100% D2O(GU)12 RNA with a deoxyribose substitution at position 6
filamentous virus14120 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] D2O, 50% H2O/50% D2OG-(GU)12-Phage50% H2O/50% D2O(GU)12 RNA sample for RDC collection
filamentous virus1570 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] D2O, 50% H2O/50% D2OU-(GU)12-Phage50% H2O/50% D2O(GU)12 RNA sample for RDC collection
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uM(GU)12natural abundance1
50 mMHEPESnatural abundance1
150 mMpotassium chloridenatural abundance1
20 uMDSSnatural abundance1
10 %D2O[U-2H]1
90 %H2Onatural abundance1
400 uM(GU)12natural abundance2
50 mMHEPESnatural abundance2
150 mMpotassium chloridenatural abundance2
20 uMDSSnatural abundance2
100 %D2O[U-2H]2
350 uM(GU)12[U-13C; U-15N]-Gua3
20 mMpotassium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
20 uMDSSnatural abundance3
10 %D2O[U-2H]3
90 %H2Onatural abundance3
350 uM(GU)12[U-13C; U-15N]-Gua4
20 mMpotassium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
20 uMDSSnatural abundance4
100 %D2O[U-2H]4
200 uM(GU)12[U-13C; U-15N]-Ura5
20 mMpotassium phosphatenatural abundance5
100 mMpotassium chloridenatural abundance5
20 uMDSSnatural abundance5
10 %D2O[U-2H]5
90 %H2Onatural abundance5
200 uM(GU)12[U-13C; U-15N]-Ura6
20 mMpotassium phosphatenatural abundance6
100 mMpotassium chloridenatural abundance6
20 uMDSSnatural abundance6
100 %D2O[U-2H]6
500 uM(GU)11.5natural abundance7
20 mMpotassium phosphatenatural abundance7
100 mMpotassium chloridenatural abundance7
20 uMDSSnatural abundance7
100 %D2O[U-2H]7
350 uM(GU)12-dG1natural abundance8
20 mMpotassium phosphatenatural abundance8
100 mMpotassium chloridenatural abundance8
20 uMDSSnatural abundance8
100 %D2O[U-2H]8
770 uM(GU)12-dU2natural abundance9
20 mMpotassium phosphatenatural abundance9
100 mMpotassium chloridenatural abundance9
20 uMDSSnatural abundance9
100 %D2O[U-2H]9
380 uM(GU)12-dG3natural abundance10
20 mMpotassium phosphatenatural abundance10
100 mMpotassium chloridenatural abundance10
20 uMDSSnatural abundance10
100 %D2O[U-2H]10
270 uM(GU)12-dU4natural abundance11
20 mMpotassium phosphatenatural abundance11
100 mMpotassium chloridenatural abundance11
20 uMDSSnatural abundance11
100 %D2O[U-2H]11
190 uM(GU)12-dG5natural abundance12
20 mMpotassium phosphatenatural abundance12
100 mMpotassium chloridenatural abundance12
20 uMDSSnatural abundance12
100 %D2O[U-2H]12
210 uM(GU)12-dU6natural abundance13
20 mMpotassium phosphatenatural abundance13
100 mMpotassium chloridenatural abundance13
20 uMDSSnatural abundance13
100 %D2O[U-2H]13
120 uM(GU)12[U-13C; U-15N]-Gua14
21 mMpotassium phosphatenatural abundance14
60 mMpotassium chloridenatural abundance14
0.02 %sodium azidenatural abundance14
0.8 mMmagnesium chloridenatural abundance14
20 mg/mLPf1 phagenatural abundance14
50 %H2Onatural abundance14
50 %D2O[U-2H]14
70 uM(GU)12[U-13C; U-15N]-Ura15
21 mMpotassium phosphatenatural abundance15
60 mMpotassium chloridenatural abundance15
0.02 uMsodium azidenatural abundance15
0.8 uMmagnesium chloridenatural abundance15
20 uMPf1 phagenatural abundance15
50 %H2Onatural abundance15
50 %D2O[U-2H]15
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMStandard conditions7.0 1 atm293 K
2100 mMLow temperature7.0 1 atm276 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7501
Bruker AVANCE IIIBrukerAVANCE III6002
Varian VNMRS DDVarianVNMRS DD6003
Varian VNMRS DDVarianVNMRS DD8004
Soln scatterType: x-ray / Buffer name: HEPES / Conc. range: 0.26-1.6 / Data analysis software list: ATSAS / Data reduction software list: IN-HOUSE SOFTWARE / Detector type: PILATUS 2M AND PILATUS 300K / Mean guiner radius: 1.3 nm / Mean guiner radius esd: 0.007 nm / Num. of time frames: 60 / Protein length: 4.7 / Sample pH: 7 / Source beamline: APS / Source beamline instrument: 12-ID-B / Source class: Y / Source type: ADVANCE PHOTON SOURCE / Temperature: 295 K

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.2 revision AAgilentcollection
TopSpin3.5Bruker Biospincollection
MestreLab (Mnova / MestReNova / MestReC)14.3.1-31739Mestrelab Researchdata analysis
NMRFAM-SPARKY1.47NMRFAMpeak picking
NMRFAM-SPARKY1.47NMRFAMchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 8 / Details: SAXS and RDC were used during refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20
Soln scatter modelMethod: HIGH TEMPERATURE DYNAMICS AT 3000 K, FOLLOWED BY SUMULATED ANNEALING FROM 3000 K TO 25 K AND A FINAL ENERGY MINIMIZATION STEP.
Conformer selection criteria: LEAST RESTRAINT VIOLATIONS
Details: STARTING MODEL WAS BEST MODEL OBTAINED AFTER CALCULATIONS WITHOUT RDC AND SCATTERING DATA.
Num. of conformers calculated: 100 / Num. of conformers submitted: 20 / Representative conformer: 1 / Software author list: SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE / Software list: X-PLOR_NIH

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