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- PDB-5uzz: Structure of wild type pre-miR21 apical loop -

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Basic information

Entry
Database: PDB / ID: 5uzz
TitleStructure of wild type pre-miR21 apical loop
Components
  • 14-mer Peptide
  • pre-miR21
KeywordsTRANSPORT PROTEIN/RNA / microRNA miR-21 oncomiR pre-miRNA / TRANSPORT PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsShortridge, M.D. / Varani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM103834 United States
American Cancer SocietyPF-13-056-01-RMC United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing.
Authors: Shortridge, M.D. / Walker, M.J. / Pavelitz, T. / Chen, Y. / Yang, W. / Varani, G.
History
DepositionFeb 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
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: pre-miR21
B: 14-mer Peptide


Theoretical massNumber of molelcules
Total (without water)11,7252
Polymers11,7252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain pre-miR21


Mass: 9912.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein/peptide 14-mer Peptide


Mass: 1812.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic22D 1H-1H NOESY
242isotropic12D 1H-1H TOCSY
252isotropic12D 1H-1H NOESY
262isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM pre-miR21, 0.8 mM ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO, 10 mM potassium phosphate, 10 mM sodium chloride, 10 mM EDTA, 100% D2Ol50_miR_complex100% D2O
solution21 mM ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO, 10 mM potassium phosphate, 10 mM sodium chloride, 95% H2O/5% D2Ofree_l5095% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMpre-miR21natural abundance1
0.8 mMARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PROnatural abundance1
10 mMpotassium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
10 mMEDTAnatural abundance1
1 mMARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PROnatural abundance2
10 mMpotassium phosphatenatural abundance2
10 mMsodium chloridenatural abundance2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1A 1:1 ratio of peptide to RNA was prepared and data collected at 37C. Preciptation was noted above 1:1 ratio and very broad lines below 37C.10 mMintermolecular NOEs6.51 atm310 K
2conditions for peptide assignments10 mMfree peptide6.51 atm310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker DRXBrukerDRX5001with tci cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8002with tci cryoprobe

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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