PDBsum entry 1k5j

Chaperone

PDB id: 1k5j

Contents

Protein chains

94 a.a. *

96 a.a. *

89 a.a. *

Waters ×147

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The crystal structure of nucleoplasmin-Core: implications for histone binding and nucleosome assembly.

Authors

S.Dutta, I.V.Akey, C.Dingwall, K.L.Hartman, T.Laue, R.T.Nolte, J.F.Head, C.W.Akey.

Ref.

Mol Cell, 2001, 8, 841-853. [DOI no: 10.1016/S1097-2765(01)00354-9]

PubMed id

11684019

Abstract

The efficient assembly of histone complexes and nucleosomes requires the participation of molecular chaperones. Currently, there is a paucity of data on their mechanism of action. We now present the structure of an N-terminal domain of nucleoplasmin (Np-core) at 2.3 A resolution. The Np-core monomer is an eight-stranded beta barrel that fits snugly within a stable pentamer. In the crystal, two pentamers associate to form a decamer. We show that both Np and Np-core are competent to assemble large complexes that contain the four core histones. Further experiments and modeling suggest that these complexes each contain five histone octamers which dock to a central Np decamer. This work has important ramifications for models of histone storage, sperm chromatin decondensation, and nucleosome assembly.

Figure 2.
Figure 2. Structure of the Np Monomer and Pentamer(A) A face view of the Np-core pentamer is shown as a ribbon diagram, viewed from the pentamer-pentamer interface. A single monomer is highlighted in cranberry. Note the prominent β hairpin that extends radially from the subunit-subunit interface.(B) An Np-core monomer is shown at higher magnification, and each β strand is labeled.(C) The Np-core monomer in (B) was rotated vert, similar 90° away from the reader to present a side view, as seen from outside the pentamer. Positions of the conserved A1 tract (red dots), β hairpin, AKDE, and GSGP loops are indicated.(D) The Np-core monomer is shown in a similar orientation as in (C), except that it is viewed from the central 5-fold axis

Figure 4.
Figure 4. Structure of the Np Decamer within Crystals(A) The Np decamer is shown, as viewed along the 5-fold axis. The two pentamers are offset by vert, similar 15°, and individual monomers within the top and bottom pentamers are labeled A′–E′ and A–E, respectively.(B) The Np decamer has an hourglass shape when viewed from the side, along a 2-fold axis. Localized negative charges are present near the pentamer-pentamer interface. In addition, a pair of opposing Lys57 residues are marked with an asterisk (see [D] and [F]).(C) A surface view of the Np pentamer is shown from within the pentamer-pentamer interface. Alternating positive (blue) and negative (red) charges that arise from Lys82 and Asp58 form an inner ring (black dots with white circles). At higher radius, Lys57 and Glu59 from the AKDE motif are revealed (see labeling key). The β hairpins form a distinctive projection.(D) A side view is shown of two Np monomers that face each other across the pentamer-pentamer interface. Lys82 and Asp58 form a pair of water-mediated, charge-based interactions that span the interface. In addition, Lys57 and Glu59 form an intramonomer salt bridge (see [F]).(E) A close-up is shown of a pair of charge-based interactions formed by Lys82, Asp58, and intervening waters.(F) A close-up is shown of an intramonomer salt bridge formed by Lys57, Glu59, and a bound water molecule. This salt bridge may neutralize potentially destabilizing interactions between opposing Lys57 residues (see [B] and [D])

The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 841-853) copyright 2001.