PDBsum entry 3b6f

Structural protein/DNA

PDB id: 3b6f

Contents

Protein chains

103 a.a.

79 a.a.

106 a.a.

101 a.a.

87 a.a.

DNA/RNA

Metals

_MN

References listed in PDB file

Key reference

Title

Site selectivity of platinum anticancer therapeutics.

Authors

B.Wu, P.Dröge, C.A.Davey.

Ref.

Nat Chem Biol, 2008, 4, 110-112. [DOI no: 10.1038/nchembio.2007.58]

PubMed id

18157123

Abstract

X-ray crystallographic and biochemical investigation of the reaction of cisplatin and oxaliplatin with nucleosome core particle and naked DNA reveals that histone octamer association can modulate DNA platination. Adduct formation also occurs at specific histone methionine residues, which could serve as a nuclear platinum reservoir influencing adduct transfer to DNA. Our findings suggest that the nucleosome center may provide a favorable target for the design of improved platinum anticancer drugs.

Figure 1.
Histone adducts occur at H3M120 and H4M84, and DNA adduct sites are numbered for cisPt (1, 5–7) and oxPt (1–4, 8, 9). The central base pair at the NCP pseudo two-fold symmetry axis is denoted by a red arrow. An apostrophe indicates the opposing NCP half. (a–c) Anomalous difference maps, contoured at 4 (a), 4.1 (b) and 3.4 (c) and superimposed on the refined models for 48-h oxPt (a,b) and cisPt (c) treatments, show platinum atom locations (black mesh). (a) View of a thin slice of the NCP. DNA strands are colored orange/cyan and histone proteins are colored blue (H3), green (H4), yellow (H2A) and red (H2B). (b) An oxPt-AG adduct. (c) cisPt adducts at GA and methionine in the NCP center. (d) DNA sequence and adduct sites (underlined) for 79 of 147 base pairs. (e) Summary of cisPt and oxPt adduct sites, with approximately one NCP half shown. Methionine sites are circled, and magenta arrows show corresponding locations in the opposing NCP half. DNA strands and histone proteins are colored as in a. (d,e) Bases (b) with major versus minor groove facing inward toward the histone octamer are colored, respectively, black and orange (d) or black and white (e). (f) Model of an oxPt adduct at the NCP center. An oxPt-GG adduct from the oligonucleotide crystal structure^17 was modified to an oxPt-GA adduct and superimposed onto the oxPt1 site adjacent to the central base pair in the high-resolution NCP crystal structure^12. The platinum (magenta) and diaminocyclohexane atoms are shown in space-filling representation to emphasize potential interactions with histone elements, such as H3K115 and H3K115' (black arrows). The atomic coordinates and structure factors for cisPt- and oxPt-treated NCP were deposited in the Protein Data Bank under accession codes 3B6F and 3B6G, respectively.

Figure 2.
NCP and naked DNA were treated with cisPt or oxPt (color-coded), followed by end labeling of the purified DNA and exonuclease III digestion (Supplementary Methods). Before fragment separation by denaturing gel electrophoresis, samples were deplatinated with thiourea to eliminate migration retardation resulting from the presence of adducts^8. This allows determination of adduct sites at approximately base-pair resolution in comparison with a modified Maxam-Gilbert purine-sequencing standard (m), in which the 3'-phosphate groups have been removed by polynucleotide kinase treatment to yield the same 3'-OH ends that arise from exonuclease cleavage. Red arrow denotes central bases. (a–c) Denaturing PAGE of exonuclease-treated DNA samples shows digest termination sites resulting from encounter of platinum adducts. Overall footprint (a) and resolved sections corresponding to the central (b) and 3' (c) regions are shown. (d) DNA sequence for 79 of 147 base pairs. Regions where the DNA minor groove faces inward, toward the histone octamer, are colored orange. Exonuclease stop sites are depicted as arrowheads adjacent to the terminal 3' nucleotide, pointing toward the apparent platinum adduct. Filled symbols indicate relatively strong termination points, and open symbols indicate moderate termination points.
*Note: In the version of this article initially published online, dash marks indicating the position of molecular weight markers in Figure 2a are missing. The error has been corrected for all versions of the article.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2008, 4, 110-112) copyright 2008.

Secondary reference #1

Title

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.

Authors

C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond.

Ref.

J Mol Biol, 2002, 319, 1097-1113. [DOI no: 10.1016/S0022-2836(02)00386-8]

PubMed id

12079350

Figure 2.
Figure 2. Solvation of NCP147. (a) Water molecules and ions associated with NCP147. The view is as in Figure 1(b). Water molecules (gold) are shown as spheres of half van der Waals radius. Manganese ions (violet) and chloride ions (green) are shown as spheres of van der Waals radius. The path of the histone chains and DNA strands are shown (H3, blue; H4, green; H2A, yellow; H2B, red; DNA strands, cyan and brown). The histone N-terminal tails are not shown in their entirety. (b) Space-filling representation of the DNA and its primary hydration layer. Water molecules (gold) with centers closer than 3.5 Å from any DNA atom center are shown. The DNA superhelix (backbones strands, cyan and brown; bases, silver) is rotated 60° around the dyad axis compared to the view in (a). (c) Minor groove "spine of hydration". Five and six-member fused rings of water molecules (red) with hydrogen bonds (broken, white) are shown in the DNA minor groove with the simulated-annealing, omit difference electron density (F[o] -F[c], 1.3s contour, yellow) superimposed.

Figure 6.
Figure 6. Specific histone-histone interparticle interactions in the NCP147 crystals. (a) Two adjacent side-chains in the histone H4 N-terminal tail, H4-R23 and H4-L22, and a Mn2+ ion (magenta) participate in extensive interactions with a highly acidic region of the H2A-H2B dimer of a neighboring nucleosome core. (b) (stereograph) A Mn2+ ion (magenta) connects H3-D77 in the H3-H4 tetramer of one particle with H2B-V45 in the H2A-H2B dimer of an adjacent particle. Both of these amino acid residues enter the coordination sphere of the divalent cation. The mean length over all six Mn2+-oxygen bonds (magenta) is 2.25 Å. Hydrogen bonds made directly between histone moieties (white) or via water molecules (yellow) are shown. (c) (stereograph) The guanidinium group of H4-R23, in a site adjacent to the Mn2+ ion of (b), makes four direct hydrogen bonds to three surrounding side-chains of the neighboring H2A-H2B dimer.

The above figures are reproduced from the cited reference with permission from Elsevier