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- PDB-7uga: Solution structure of NPSL2 -

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Basic information

Entry
Database: PDB / ID: 7uga
TitleSolution structure of NPSL2
ComponentsNPSL2 RNA (43-MER)
KeywordsRNA / Internal loop / apical loop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SOLUTION SCATTERING / molecular dynamics
AuthorsLiu, Y. / Keane, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM138279 United States
Citation
Journal: J.Mol.Biol. / Year: 2022
Title: Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA.
Authors: Liu, Y. / Munsayac, A. / Hall, I. / Keane, S.C.
#1: Journal: Biorxiv / Year: 2022
Title: Solution structure of NPSL2, a regulatory element in the oncomiR-1 RNA
Authors: Liu, Y. / Munsayac, A. / Hall, I. / Keane, S.C.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_id_ISSN / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: NPSL2 RNA (43-MER)


Theoretical massNumber of molelcules
Total (without water)13,8061
Polymers13,8061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40target function
RepresentativeModel #1lowest energy

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Components

#1: RNA chain NPSL2 RNA (43-MER)


Mass: 13806.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: in vitro transcription vector pT7-TP(deltai) (others)

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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
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H NOESY
134anisotropic22D 1H-13C HSQC
144isotropic22D 1H-13C HSQC
153anisotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM 1H NPSL2 RNA (43-MER), 100% D2O1H_aromatic100% D2O
solution2500 uM 1H NPSL2 RNA (43-MER), 90% H2O/10% D2O1H_imino90% H2O/10% D2O
solution3500 uM 1H NPSL2 RNA (43-MER), 90% H2O/10% D2O2H90% H2O/10% D2O
solution4500 uM 1H NPSL2 RNA (43-MER), 12.5 mg/mL unlabeled Pf1 phage, 90% H2O/10% D2O15N,13C-A,G90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMNPSL2 RNA (43-MER)1H1
500 uMNPSL2 RNA (43-MER)1H2
500 uMNPSL2 RNA (43-MER)1H3
500 uMNPSL2 RNA (43-MER)1H4
12.5 mg/mLPf1 phageunlabeled4
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 288.15 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJJohnsonchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 20

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