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- PDB-7kuc: Ax1 Domain of VEGF Readthrough Element -

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Basic information

Entry
Database: PDB / ID: 7kuc
TitleAx1 Domain of VEGF Readthrough Element
ComponentsVEGF Ax1
KeywordsRNA / Stop codon readthrough / VEGF mRNA / stem-loop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / simulated annealing
Model detailsNMR Structure
AuthorsD'Souza, V.M. / Wagner, N.O. / Edwards, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)55108516 United States
National Science Foundation (NSF, United States)1144152 United States
CitationJournal: To Be Published
Title: Stop codon readthrough in VEGF-A is regulated by complex signals
Authors: Wagner, N.O. / Edwards, J.E. / Abramovich, J. / Gupta, P. / Swaminathan, H. / Rouskin, S. / D'Souza, V.M.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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

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Assembly

Deposited unit
A: VEGF Ax1


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10010 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain VEGF Ax1


Mass: 5215.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D NOESY
222anisotropic21H-13C HMQC
333anisotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM RNA, 100% D2OD2O_NOESY_sample100% D2O
solution21 mM [U-13C] RNA, 100% D2OHMQC_sample100% D2O
solution31 mM RNA, 10%D2O 90%H2OH2O_NOESY_sample10%D2O 90%H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRNAnatural abundance1
1 mMRNA[U-13C]2
1 mMRNAnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150MM KCL mMCondition_15.6ambient 311 K
250MM KCL mMCondition_25.6ambient 311 K
350MM KCL mMCondition_35.6ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Ascend800BrukerAscend8008001
Bruker UltraShield700PlusBrukerUltraShield700Plus7002

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Processing

NMR software
NameVersionDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJBruce A. Johnsonchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIH3.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 3
Details: First round of structure calculation was conducted with distance and dihedral angle restraints only. Second round was performed with electrostatics using both high temperature annealing and ...Details: First round of structure calculation was conducted with distance and dihedral angle restraints only. Second round was performed with electrostatics using both high temperature annealing and low temperature annealing.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 10 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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