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- PDB-6pk9: Solution Structure of lncRNA (LINK-A) 20-nt Hexaloop Hairpin -

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Basic information

Entry
Database: PDB / ID: 6pk9
TitleSolution Structure of lncRNA (LINK-A) 20-nt Hexaloop Hairpin
ComponentsRNA (5'-R(*GP*GP*AP*GP*GP*GP*UP*AP*GP*AP*CP*UP*CP*GP*CP*UP*CP*UP*CP*C)-3')
KeywordsREPLICATION / RNA / LINK-A / lncRNA / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAmado, A.Y. / Walker, M. / Varani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)62-8160 United States
CitationJournal: To Be Published
Title: Structure of the lncRNA LINK-A Hexaloop Hairpin in PI(3,4,5)P3 Interaction
Authors: Amado, A.Y. / Walker, M. / Varani, G.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*GP*GP*GP*UP*AP*GP*AP*CP*UP*CP*GP*CP*UP*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,4151
Polymers6,4151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*GP*GP*GP*UP*AP*GP*AP*CP*UP*CP*GP*CP*UP*CP*UP*CP*C)-3') / LINK-A


Mass: 6414.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-1H NOESY
225isotropic22D 1H-1H TOCSY
235isotropic22D 1H-1H NOESY
345isotropic22D 1H-1H NOESY
156isotropic22D 1H-15N HSQC
267isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution40.9 mM RNA, 90% H2O/10% D2OLINK-A-190% H2O/10% D2O
solution50.6 mM RNA, 100% D2OLINK-A-2100% D2O
solution60.5 mM [U-13C; U-15N] RNA, 90% H2O/10% D2OLINK-A-390% H2O/10% D2O
solution70.5 mM [U-13C; U-15N] RNA, 100% D2OLINK-A-4100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMRNAnatural abundance4
0.6 mMRNAnatural abundance5
0.5 mMRNA[U-13C; U-15N]6
0.5 mMRNA[U-13C; U-15N]7
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Mixing time = 200 ms20 mM Sodium Phosphate + 0.01 mM EDTA Not definedconditions-16.0 1 atm278 K
2100% D2O; mixing time = 100 msnone Not definedconditions-26.0 1 atm298 K
3100% D2O; mixing time = 300 msnone Not definedconditions-36.0 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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