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- PDB-1y9h: Methylation of cytosine at C5 in a CpG sequence context causes a ... -

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Basic information

Entry
Database: PDB / ID: 1y9h
TitleMethylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement
Components
  • 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3'
  • 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'
KeywordsDNA / conformational switch / cytosine methylation / p53 mutation hot spot / DNA adduct / benzo[a]pyrene / BPDE
Function / homology1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics matrix relaxation
AuthorsZhang, N. / Lin, C. / Huang, X. / Kolbanovskiy, A. / Hingerty, B.E. / Amin, S. / Broyde, S. / Geacintov, N.E. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation ...Title: Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement.
Authors: Zhang, N. / Lin, C. / Huang, X. / Kolbanovskiy, A. / Hingerty, B.E. / Amin, S. / Broyde, S. / Geacintov, N.E. / Patel, D.J.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 24, 2024Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_PDB_caveat / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_validate_close_contact / struct_conn
Item: _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair_step.twist
Remark 999SEQUENCE C10 atom of BP is covalently bonded to N2 atom of G6 in Chain A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3'
B: 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0273
Polymers6,7222
Non-polymers3041
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 9all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: DNA chain 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3'


Mass: 3268.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BP ATTACHED TO G6, Methylation of C5
#2: DNA chain 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'


Mass: 3454.258 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-BAP / 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE


Mass: 304.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: 11mer DNA duplex with MeC5 and [BP]G6 modified, H2O and D2O
Solvent system: H2O and D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.8 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing, molecular dynamics matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable ...Conformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 9 / Conformers submitted total number: 9

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