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- PDB-1ync: NMR structure of the apoB mRNA stem-loop and its interaction with... -

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Basic information

Entry
Database: PDB / ID: 1ync
TitleNMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor
Componentsapolipoprotein B mRNA
KeywordsRNA / RNA editing / apoB mRNA / APOBEC1 / ACF / NMR structure
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / CYANA, AMBER7
AuthorsMaris, C. / Masse, J. / Allain, F.H. / Chester, A. / Navaratnam, N.
CitationJournal: Rna / Year: 2005
Title: NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor.
Authors: Maris, C. / Masse, J. / Chester, A. / Navaratnam, N. / Allain, F.H.
History
DepositionJan 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE This entry 1YNC has unedited RNA with C6666 in syn conformation. The edited apoB mRNA ...SEQUENCE This entry 1YNC has unedited RNA with C6666 in syn conformation. The edited apoB mRNA sequence leading to the truncated protein has the same accession number since it comes from the same gene. The numbering starts at 6656 on the apoB mRNA sequence but for experimental reason the first and last two nucleotides GG and CC were added, which do not belong to the native sequence, the number starts at 6654.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: apolipoprotein B mRNA


Theoretical massNumber of molelcules
Total (without water)9,8911
Polymers9,8911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #12closest to the average

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Components

#1: RNA chain apolipoprotein B mRNA / apoB mRNA


Mass: 9890.887 Da / Num. of mol.: 1 / Fragment: Editing site of APOB enzyme / Source method: obtained synthetically
Details: In vitro T7 polymerase transcription, The sequence of this RNA naturally exists in Homo sapiens (human)
References: GenBank: 4502152

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
141DQF-COSY
252HNN COSY
161(H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O
21.2 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; Selective U 15N&13C labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O
31.0 mMapoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; Selective A 15N&13C labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O
41.0 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; Selective G&C 15N&13C labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O
51.5 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; full 15N&C13 labeling; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM Na2HPO4 5.8 1 atm313 K
210 mM Na2HPO4 5.8 1 atm278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guentert, P.structure solution
XwinNMR2004Brukercollection
Sparky2002Goddard, T. D. and Kneller, D. Gdata analysis
X-EASY2001Bartels, C.data analysis
Amber7Ponder, J.W. and Case, D.A.refinement
RefinementMethod: CYANA, AMBER7 / Software ordinal: 1 / Details: calculation in vacuum condition
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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