PDBsum entry 1kx5

Structural protein/DNA

PDB id: 1kx5

Contents

Protein chains

135 a.a. *

102 a.a. *

128 a.a. *

122 a.a. *

DNA/RNA

Metals

_MN ×14

_CL ×4

Waters ×3130

* Residue conservation analysis

References listed in PDB file

Key reference

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

Abstract

Solvent binding in the nucleosome core particle containing a 147 base pair, defined-sequence DNA is characterized from the X-ray crystal structure at 1.9 A resolution. A single-base-pair increase in DNA length over that used previously results in substantially improved clarity of the electron density and accuracy for the histone protein and DNA atomic coordinates. The reduced disorder has allowed for the first time extensive modeling of water molecules and ions. Over 3000 water molecules and 18 ions have been identified. Water molecules acting as hydrogen-bond bridges between protein and DNA are approximately equal in number to the direct hydrogen bonds between these components. Bridging water molecules have a dual role in promoting histone-DNA association not only by providing further stability to direct protein-DNA interactions, but also by enabling formation of many additional interactions between more distantly related elements. Water molecules residing in the minor groove play an important role in facilitating insertion of arginine side-chains. Water structure at the interface of the histones and DNA provides a means of accommodating intrinsic DNA conformational variation, thus limiting the sequence dependency of nucleosome positioning while enhancing mobility. Monovalent anions are bound near the N termini of histone alpha-helices that are not occluded by DNA phosphate groups. Their location in proximity to the DNA phosphodiester backbone suggests that they damp the electrostatic interaction between the histone proteins and the DNA. Divalent cations are bound at specific sites in the nucleosome core particle and contribute to histone-histone and histone-DNA interparticle interactions. These interactions may be relevant to nucleosome association in arrays.

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 reprinted by permission from Elsevier: J Mol Biol (2002, 319, 1097-1113) copyright 2002.

Secondary reference #1

Title

Crystal structure of the nucleosome core particle at 2.8 a resolution.

Authors

K.Luger, A.W.Mäder, R.K.Richmond, D.F.Sargent, T.J.Richmond.

Ref.

Nature, 1997, 389, 251-260. [DOI no: 10.1038/38444]

PubMed id

9305837

Figure 2.
Figure 2 H3-H4 histone-fold pair. The 1-L1- 2-L2- 3 structural elements are shown. A pseudodyad axis of symmetry runs vertically through SHL1.5. Side chains that make hydrogen bonds or hydrophobic interactions with the DNA backbones, and arginines inserted in the minor groove are shown. Main-chain-to-DNA-phosphate hydrogen bonds are shown in magenta. Leucine 65 is in contact with a thymidine methyl group (yellow bond). Two of three arginine-threonine pairs are hydrogen bonded (cyan bond). b, H2A-H2B histone-fold pair. As in a, except that the pseudodyad axis runs through SHL4.5. c, H3-H4 L1L2 DNA-binding site. The H3 L1 and H4 L2 loops make 3 hydrogen bonds (cyan) with each other in a parallel -structure. The L2 loop contains buried hydrogen bonds (cyan) between H4-R78 and H4-D85. The hydrogen-bonding interactions (magenta) between protein and DNA-phosphate groups involve both main-chain amide atoms and side-chain atoms. d, H2A-H2B L1L2 DNA-binding site. In contrast to the H3 L1 and H4 L2 loops, the other three L1L2 sites have only one well formed -structure hydrogen bond, as for H2A L1 and H2B L2 shown here (cyan). An arginine (H2B-R83) hydrogen bonds to a phosphate group instead of an acidic side chain (H2B-E90), as occurs at the homologous sites in the other L1L2 loops. e, H3'-H3 4-helix bundle. The H3-H4 histone pairs form the tetramer through the interaction of the C-terminal halves of the 2 helices and the 3 helix of H3' and H3 across the molecular dyad axis. Histidine 113' makes a buried hydrogen bond to link the H3 molecules. In addition, several hydrophobic interactions occur. f, H2B-H4 4-helix bundle. The H2A-H2B dimer assembles into the histone octamer through the interaction of H2B with H4. The hydrogen bond of H4-H75 to H2B-E90 is analogous to that in H3'-H3, but is not buried here because of the orientation of H2B-R83. Across the pseudo-twofold axis, however, H2B-Y80 replaces the H4 histidine and, together with H4-Y72 and H4-Y88, forms a hydrophobic cluster.

Figure 3.
Figure 3 Histone tails between DNA gyres. The H2B (red) and H3 (blue) N-terminal tails pass through channels in the DNA superhelix (white) formed by aligned minor grooves. b, H3 tail segment in minor-groove channel. The H3 tail sequence HRYRP passes through the juxtaposed minor grooves of SHL -7 (DNA terminus) and SHL1 (DNA centre). The electron density (magenta) clearly identifies the conformation of these amino acids. c, H4 tail bound to the H2A-H2B dimer. The electrostatic surface of the nucleosome core particle shows an intensely negatively charged region (bright red) near the centre of its exposed protein face. Amino acids 16-25 of the H4 tail lie on this region of the H2A-H2B dimer, which contains 7 clustered acidic side chains. The orientation of the particle is as for Fig. 1d .

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd

Secondary reference #2

Title

Dna-Dependent divalent cation binding in the nucleosome core particle.

Authors

C.A.Davey, T.J.Richmond.

Ref.

Proc Natl Acad Sci U S A, 2002, 99, 11169-11174. [DOI no: 10.1073/pnas.172271399]

PubMed id

12169666

Figure 1.
Fig 1. Divalent cation binding sites on nucleosomal DNA. (A) Location of the Mn2+ binding sites in one half of the DNA superhelix (79 of 147 bp, 0 indicates the central base pair and 5' and 3' labels indicate the DNA terminus). All filled sites ( ) occur at GG or GC base pair steps in the DNA major groove except for one site in the minor groove. The site numbers, including vacant GG and GC base pair steps (x), correspond to Table 1. DNA bases are shaded according to whether the major (gray) or minor (white) groove faces inward. The DNA backbone is colored according to the value of the base pair-step roll parameter as indicated (Roll). (B and C) Electron density for Mn2+ sites 1-GG and 5-GC, respectively. Anomalous difference electron density (green, 4 contour) denotes the location of the Mn2+ ions, and simulated annealing, omit difference electron density (yellow, F[o] - F[c] 1.5 and 2 contours, respectively) corresponds to the positions of the metal-coordinated water molecules (five first shell, one second shell). Coordination bonds (magenta) between metal ion (magenta) and water molecules (red) are shown in the context of the surrounding base pair steps.

Figure 2.
Fig 2. Three-bond and four-bond modes of Mn2+ binding in the DNA major groove. (A and C) The three-bond mode is shown for sites 1-GG and 5-GC, respectively. (B and D) The four-bond mode is shown for sites 4-GG and 6-GC, respectively. The guanine N7 and O6 atoms defining the metal binding mode and the contributing bases are labeled (G' indicates the complementary base to C in the GC step). A nonzero shift parameter for a base pair step is visualized as a deviation of the double helix axis (green). Coordination bonds (magenta) between metal ion (magenta) and water molecules (red), and hydrogen bonds (yellow) between bases and first and second shell, coordinated water molecules are shown. (E) The site 1-GG (A) is shown with its full hydrogen bonding network. A hydrogen bond occurs between the N7 atom of the adenine base (5' A) adjacent to the GG base step and a metal-coordinated water molecule, contributing to the orientation of the metal ion-hydrate. (F) Site 3-GG binds Mn2+ in the same three-bond mode as site 1-GG, but lacks the additional coordination shell bond from the adjacent thymine base (5' T).

Secondary reference #3

Title

The structure of DNA in the nucleosome core.

Authors

T.J.Richmond, C.A.Davey.

Ref.

Nature, 2003, 423, 145-150. [DOI no: 10.1038/nature01595]

PubMed id

12736678

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 73%.

Figure 1.
Figure 1: Superhelical path and base-pair-step parameters for NCP147 DNA. a, Structural alignment of the NCP147 (gold) and best-fit, ideal superhelix (red) paths. The NCP147 DNA structure is superimposed (gold). The left view is down the superhelix axis and the right view is rotated 90° around the pseudo-two-fold axis (vertical). b, Roll, tilt, shift, slide and twist base-pair-step parameters. The base-pair-step values plotted are the means for the two halves of the symmetrical sequence (shown above, with the dyad position labelled '0'). The iCAT and iSAT curves (red) show the roll and tilt contributions to the ideal superhelix curvature. The minor-groove blocks show base-pair-step shift alternation (pink in shift and tilt) or kinks (orange in roll, slide and twist). The primary bound-phosphate groups are indicated above the base sequence by pointers (numbered as the 5' phosphate of the adjacent base) showing the strand direction (dark, 3' arrow 5'; light, 5' arrow 3') and the interacting histone motif (L1, loop 1; L2, loop 2; A1, 1).

Figure 2.
Figure 2: DNA bending in the NCP147 DNA. Structures (left) and schematic representations (right) stress uniformity of curvature in the major-groove blocks (red) (a), and alternating shift values (b) and localization of curvature in kinks in minor-groove blocks (c) (yellow for one representative double-helical turn). Also indicated are the primary bound-phosphate groups (green), the block-junction phosphate groups (white) and the DNA axes for the NCP147 (gold) and ideal (white) superhelices. The contributions of base-pair-step curvature to superhelix bending are listed with base-pair numbers (centre).

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd