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- PDB-1eln: SOLUTION STRUCTURE OF A MODIFIED HUMAN TELOMERE FRAGMENT (STRUCTU... -

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Entry
Database: PDB / ID: 1eln
TitleSOLUTION STRUCTURE OF A MODIFIED HUMAN TELOMERE FRAGMENT (STRUCTURE "S")
Components5'-D(*CP*CP*CP*TP*AP*AP*(5CM)P*CP*CP*TP*AP*AP*CP*CP*CP*UP*AP*AP*CP*CP*CP*T)-3'
KeywordsDNA / DNA solution structure / i-motif / interacting loops / loop motions / telomere
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NMR-based simulated annealing
AuthorsPhan, A.T. / Gueron, M. / Leroy, J.-L.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere.
Authors: Phan, A.T. / Gueron, M. / Leroy, J.L.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*CP*TP*AP*AP*(5CM)P*CP*CP*TP*AP*AP*CP*CP*CP*UP*AP*AP*CP*CP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)6,5211
Polymers6,5211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations, lowest energy

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Components

#1: DNA chain 5'-D(*CP*CP*CP*TP*AP*AP*(5CM)P*CP*CP*TP*AP*AP*CP*CP*CP*UP*AP*AP*CP*CP*CP*T)-3' / TELOMERE FRAGMENT


Mass: 6521.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cytosines C1, 2, 3 19, 20, and 21 protonated at N3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY, COSY, TOCSY, 31P-1H HETERO-TOCSY, 13C-1H HSQC, HMBC, JRHMBC
NMR detailsText: The structure was determined using 2D homonuclear and natural abundance heteronuclear techniques at temperatures 263-303.

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Sample preparation

DetailsContents: 1.5-4 mM of unlabeled DNA / Solvent system: water
Sample conditionsIonic strength: ~10mM NaCl / pH: 5 / Pressure: ambient / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Brunger, A.T. / Classification: refinement
RefinementMethod: NMR-based simulated annealing / Software ordinal: 1
Details: chemical shifts are in the same table as for the related structure 1EL2
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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