PDBsum entry 3c1c

Structural protein/DNA

PDB id: 3c1c

Contents

Protein chains

98 a.a. *

78 a.a. *

105 a.a. *

93 a.a. *

84 a.a. *

DNA/RNA

Waters ×284

* Residue conservation analysis

PDB id:

3c1c

Name:

Structural protein/DNA

Title:

The effect of h3 k79 dimethylation and h4 k20 trimethylation on nucleosome and chromatin structure

Structure:

Histone h3-like. Chain: a, e. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a type 1. Chain: c, g. Engineered: yes.

Source:

Xenopus laevis. Clawed frog,common platanna,platanna. Organism_taxid: 8355. Gene: histone h3. Expressed in: escherichia coli. Gene: histone h4. Gene: histone h2a. Xenopus (silurana) tropicalis. Western clawed frog.

Resolution:

3.15Å R-factor: 0.220 R-free: 0.290

Authors:

X.Lu,M.Simon,J.Chodaparambil,J.Hansen,K.Shokat,K.Luger

Key ref:

X.Lu et al. (2008). The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Biol, 15, 1122-1124. PubMed id: 18794842 DOI: 10.1038/nsmb.1489

Date:

22-Jan-08 Release date: 07-Oct-08

Protein chains

P84233  (H32_XENLA) -  Histone H3.2 from Xenopus laevis

Seq: 136 a.a.

Struc: 98 a.a.*

Protein chain

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 78 a.a.

Protein chains

P06897  (H2A1_XENLA) -  Histone H2A type 1 from Xenopus laevis

Seq: 130 a.a.

Struc: 105 a.a.*

Protein chains

Q28D68  (Q28D68_XENTR) -  Histone H2B from Xenopus tropicalis

Seq: 126 a.a.

Struc: 93 a.a.

Protein chain

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 84 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-T-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 146 bases

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-T-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 146 bases

DOI no: 10.1038/nsmb.1489

Nat Struct Biol 15:1122-1124 (2008)

PubMed id: 18794842

The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.

X.Lu, M.D.Simon, J.V.Chodaparambil, J.C.Hansen, K.M.Shokat, K.Luger.

ABSTRACT

Histone methylation regulates chromatin function dependent on the site and degree of the modification. In addition to creating binding sites for proteins, methylated lysine residues are likely to influence chromatin structure directly. Here we present crystal structures of nucleosomes reconstituted with methylated histones and investigate the folding behavior of resulting arrays. We demonstrate that dimethylation of histone H3 at lysine residue 79 locally alters the nucleosomal surface, whereas trimethylation of H4 at lysine residue 20 affects higher-order structure.

Selected figure(s)

Figure 1.
(a) Location of H3K79 and H4K20 (red) on the unmodified NCP structure (surface representation; PDB 1AOI). Histones H2A, H2B, H3 and H4 are shown in light yellow, red, blue and green, respectively. (b) H3K[c]79me2 adopts an alternative side chain conformation. The structures of the NCP containing H3[c]79me2 (light blue and light green) were superimposed onto unmodified NCP (dark blue and dark green). H3K[c]79me2 is shown in yellow and unmodified K79 is shown in red. (c) Electrostatic potential of the same region in NCP containing H3K[c]79me2 as shown in b. (d) The equivalent region for unmodified NCP. Red indicates negative surface potential and blue indicates positive surface potential, scaled from -15 to +15. Note the small hydrophobic cavity (indicated with an arrow in c) that is uncovered by the reorientation of H3K[c]79me2. (e) Superposition of nucleosomes with H4K[c]20me3 (light green, light blue) with unmodified NCP (dark green, dark blue). (f) Superposition of H4 tails from published nucleosome structures. Blue, human NCP (PDB 2CV5)^19; yellow, X. laevis NCP (PDB 1KX5)^20; red, acetylated histone H4 (PDB 16EI)^21; green, NCP with H4K[c]20me3 (this work, PDB 3C1B).

Figure 2.
(a–c) Analysis was carried out in TEN buffer (a), in buffer contain 1 mM MgCl[2] (b) and 1.5 mM MgCl[2] (c). (d) Self-association of unmodified, H3K[c]79me2 and H4K[c]20Me3 nucleosomal arrays. Symbols in a–d: circle , H3K[c]79me2 nucleosomal array; , unmodified nucleosomal array; triangle , H4K[c]20Me3 nucleosomal array. The experiments were repeated three times with identical results (see also Supplementary Fig. 3); one representative experiment is shown. Error bars are s.d.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 1122-1124) copyright 2008.