PDBsum entry 1hq3

DNA binding protein

PDB id: 1hq3

Contents

Protein chains

106 a.a. *

92 a.a. *

95 a.a. *

83 a.a. *

Ligands

PO4 ×5

Metals

_CL ×22

Waters ×437

* Residue conservation analysis

PDB id:

1hq3

Name:

DNA binding protein

Title:

Crystal structure of the histone-core-octamer in kcl/phosphate

Structure:

Histone h2a-iv. Chain: a, e. Histone h2b. Chain: b, f. Histone h3. Chain: c, g. Histone h4-vi. Chain: d, h

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Organelle: chick-erythrocyte nuclei. Other_details: extracted as part of octamer in kcl/phosphate. Other_details: extracted as part of octamer in kcl/phosphate

Biol. unit:

Tetramer (from PQS)

Resolution:

2.15Å R-factor: 0.214 R-free: 0.253

Authors:

L.Chantalat,J.M.Nicholson,S.J.Lambert,A.J.Reid,M.J.Donovan, C.D.Reynolds,C.M.Wood,J.P.Baldwin

Key ref:

L.Chantalat et al. (2003). Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 A resolution. Acta Crystallogr D Biol Crystallogr, 59, 1395-1407. PubMed id: 12876341 DOI: 10.1107/S0907444903011880

Date:

14-Dec-00 Release date: 24-Jan-01

Protein chains

P02263  (H2A4_CHICK) -  Histone H2A-IV from Gallus gallus

Seq: 129 a.a.

Struc: 106 a.a.

Protein chains

P0C1H5  (H2B7_CHICK) -  Histone H2B 7 from Gallus gallus

Seq: 126 a.a.

Struc: 92 a.a.*

Protein chains

P84229  (H32_CHICK) -  Histone H3.2 from Gallus gallus

Seq: 136 a.a.

Struc: 95 a.a.

Protein chains

P62801  (H4_CHICK) -  Histone H4 from Gallus gallus

Seq: 103 a.a.

Struc: 83 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1107/S0907444903011880

Acta Crystallogr D Biol Crystallogr 59:1395-1407 (2003)

PubMed id: 12876341

Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 A resolution.

L.Chantalat, J.M.Nicholson, S.J.Lambert, A.J.Reid, M.J.Donovan, C.D.Reynolds, C.M.Wood, J.P.Baldwin.

ABSTRACT

The structure of the native chicken histone octamer, crystallized in 2 M KCl, 1.35 M potassium phosphate pH 6.9, has been refined at 2.15 A resolution to a final R factor of 21.4% and an R(free) of 25.2%. Unique crystal-packing interactions between histone-core octamers are strong and one of them (area 4000 A(2)) involves two chloride ions and direct interactions between six acidic amino-acid residues on one octamer and the equivalent number of basic residues on the next. These interactions are on the structured part of the octamer (not involving tails). Five phosphate ions, 23 chloride ions and 437 water molecules have been identified in the structure. The phosphate and some chloride ions bind to basic amino-acid residues that interact with DNA in the nucleosome. The binding of most of the anions and the packing interactions are unique to these crystals. In other respects, and including the positions of four chloride ions, the octamer structure is very close to that of octamers in nucleosome-core particle crystals, particularly with respect to 'docking' sequences of the histone H2As and H4s. These sequences together with the H2B-H4 four-helix bundles stabilize the histone structure in the nucleosome and prevent the dissociation of the (H2A-H2B) dimers from the (H3-H4)(2) tetramer. Possible reasons why this happens at high salt in the absence of DNA are given.

Selected figure(s)

Figure 5.
Figure 5 Stereo figures of amino-acid residues interacting with chlorides a. Interactions of chloride k with Arg69, Arg72 and Gln68 in histone H3' (see also Fig. 1-). (b) The extra interaction between the docking sequence of histone H4' at Arg95 and the docking sequence of histone H2A at Thr101, involving chloride q (green) and water molecules (black). Note the short parallel- structure coupling residues Val100, Thr101 and Ile102 of histone H2A to residues Thr96, Leu97 and Tyr98 of histone H4'. (c) Chloride q provides the extra inter-docking sequence interaction of Fig. 4-(b) and chloride w and water molecules provide the coupling between the H4 docking sequence and the 2 helix of histone H2B'. Note the two parallel -sheet regions. Chloride ions are shown in green and water molecules in black.

Figure 6.
Figure 6 Superposition of the H2A (residues 97-116) and H4' (residues 92-102) docking sequences for the following octamer structures: S1, the octamer in KCl/phosphate (blue); S2, the octamer in ammonium sulfate of Arents et al. (1991[Arents, G., Burlingame, R. W., Wang, B. C., Love, W. E. & Moudrianakis, E. N. (1991). Proc. Natl Acad. Sci. USA, 88, 10148-10152.]) (yellow); S3, the octamer in the nucleosome core particle of Luger et al. (1997[Luger, K., Maeder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. (1997). Nature (London), 389, 251-260.]) (red); S4, the octamer in the nucleosome core particle of Harp et al. (2000[Harp, J. M., Hanson, B. L., Timm, D. E. & Bunick, G. J. (2000). Acta Cryst. D56, 1513-1534.]) (green). Notice the similarity between the structures as well as some differences, particularly for histone H4'.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 1395-1407) copyright 2003.

Figures were selected by an automated process.