PDBsum entry 5avb

DNA binding protein/DNA

PDB id: 5avb

Contents

Protein chains

99 a.a.

82 a.a.

106 a.a.

97 a.a.

87 a.a.

DNA/RNA

Metals

_MN ×14

Waters ×197

PDB id:

5avb

Name:

DNA binding protein/DNA

Title:

Human nucleosome core particle

Structure:

Histone h3.1. Chain: a, e. Synonym: histone h3/a,histone h3/b,histone h3/c,histone h3/d,histone h3/f,histone h3/h,histone h3/i,histone h3/j,histone h3/k,histone h3/l. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hist1h3a, h3fa, hist1h3b, h3fl, hist1h3c, h3fc, hist1h3d, h3fb, hist1h3e, h3fd, hist1h3f, h3fi, hist1h3g, h3fh, hist1h3h, h3fk, hist1h3i, h3ff, hist1h3j, h3fj. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768. Gene: hist1h4a, h4/a, h4fa, hist1h4b, h4/i, h4fi, hist1h4c, h4/g,

Resolution:

2.40Å R-factor: 0.199 R-free: 0.236

Authors:

M.Wakamori,Y.Fujii,T.Umehara,S.Yokoyama

Key ref:

M.Wakamori et al. (2015). Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Sci Rep, 5, 17204. PubMed id: 26607036 DOI: 10.1038/srep17204

Date:

12-Jun-15 Release date: 23-Dec-15

Protein chains

P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens

Seq: 136 a.a.

Struc: 99 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 82 a.a.

Protein chains

P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E from Homo sapiens

Seq: 130 a.a.

Struc: 106 a.a.

Protein chains

P06899  (H2B1J_HUMAN) -  Histone H2B type 1-J from Homo sapiens

Seq: 126 a.a.

Struc: 97 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 87 a.a.

DNA/RNA chains

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-A-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 147 bases

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-A-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 147 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.?

DOI no: 10.1038/srep17204

Sci Rep 5:17204 (2015)

PubMed id: 26607036

Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation.

M.Wakamori, Y.Fujii, N.Suka, M.Shirouzu, K.Sakamoto, T.Umehara, S.Yokoyama.

ABSTRACT

Post-translational modifications (PTMs) of histones, such as lysine acetylation of the N-terminal tails, play crucial roles in controlling gene expression. Due to the difficulty in reconstituting site-specifically acetylated nucleosomes with crystallization quality, structural analyses of histone acetylation are currently performed using synthesized tail peptides. Through engineering of the genetic code, translation termination, and cell-free protein synthesis, we reconstituted human H4-mono- to tetra-acetylated nucleosome core particles (NCPs), and solved the crystal structures of the H4-K5/K8/K12/K16-tetra-acetylated NCP and unmodified NCP at 2.4 Å and 2.2 Å resolutions, respectively. The structure of the H4-tetra-acetylated NCP resembled that of the unmodified NCP, and the DNA wrapped the histone octamer as precisely as in the unmodified NCP. However, the B-factors were significantly increased for the peripheral DNAs near the N-terminal tail of the intra- or inter-nucleosomal H4. In contrast, the B-factors were negligibly affected by the H4 tetra-acetylation in histone core residues, including those composing the acidic patch, and at H4-R23, which interacts with the acidic patch of the neighboring NCP. The present study revealed that the H4 tetra-acetylation impairs NCP self-association by changing the interactions of the H4 tail with DNA, and is the first demonstration of crystallization quality NCPs reconstituted with genuine PTMs.