BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 25882

Title: Structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A   PubMed: 26929332

Authors: Woo, Christina; Li, Zhenwu; Paulson, Eric; Herzon, Seth

Citation: Woo, Christina; Li, Zhenwu; Paulson, Eric; Herzon, Seth. "Structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A"  Proc. Natl. Acad. Sci. U.S.A. 113, 2851-2856 (2016).

Assembly members:
DNA_(5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3'), polymer, 8 residues, Formula weight is not available
(1R,1'R,2S,2'S,3R,3'R,5a'R,10a'R,11aS)-2'-[(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)oxy]-2,2'-diethyl-11,11'-dihydrazinyl-6,6',9,9'-tetrahydroxy-4,4',5,5',10,10'-hexaoxo-1,1'-bis{[2,4,6-trideoxy-4-(dimethylamino)-beta-L-arabino-hexopyranosyl]oxy}-2,2',3,3',4,4',5,5',5a',8',10,10',10a',11a-tetradecahydro-1H,1'H-3,3'-bibenzo[b]fluoren-2-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside, non-polymer, 1375.468 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_(5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3'): GCTATAGC

Data sets:
Data typeCount
1H chemical shifts234

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3')1
2DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3')1
3lomaiviticin A2

Entities:

Entity 1, DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3') 8 residues - Formula weight is not available

1   DGDCDTDADTDADGDC

Entity 2, lomaiviticin A - C68 H90 N6 O24 - 1375.468 Da.

1   4JF

Samples:

sample_1: DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP))-3') 2.2 uM; lomaiviticin A 1.1 uM; sodium phospate 10 mM; sodium chloride 25 mM; D2O, [U-2H], 100%

sample_2: DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP))-3') 2.2 uM; lomaiviticin A 1.1 uM; sodium phospate 10 mM; sodium chloride 25 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 24 mM; pH: 7.5; pressure: 1 atm; temperature: 297 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1

Software:

AMBER v14, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

NMR spectrometers:

  • Agilent DD2 800 MHz

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