Physical characteristics of the CENP-A nucleosome. (A) Pairwise alignment of human CENP-A (NCBI Protein accession no. NP_001800.1) and H3.1 (NCBI Protein accession no. NP_003522.1) sequences, showing the secondary structural features of CENP-A. Residues that are 100% conserved are shown in red. (B) Overlay of nucleic acid sequences structured within the CENP-A nucleosome crystal (derived from PDB accession no. 3AN2) with those from the H3.1 nucleosome structure (PDB accession no. 5Y0C), respectively, showing loss of structured DNA termini, indicating unwrapping, in the CENP-A nucleosome. (C) Structural superposition of the complete CENP-A (PDB accession no. 3AN2) and histone H3.1 nucleosome (PDB accession no. 5Y0C). The inset shows a zoomed view of the loop 1 distension in the CENP-A nucleosome vis-à-vis the H3 nucleosome. (D) Comparison of CENP-A:H4 as heterotetramer (PDB accession no. 3NQJ) compared with CENP-A:H4 in nucleosomes (PDB accession no. 3AN2), with special emphasis on hydrophobic stitching. Representation is rotated 180° to show two opposite surfaces: i, nucleosome surface; and ii, nucleosome interior. CENP-A-H4 in the tetramer structure as well as nucleosomal CENP-A-H4 show a similar occupancy when viewed on the nucleosome surface (i). However, viewed from the interior (ii), nucleosomal CENP-A-H4 is predominantly seen, indicating that CENP-A-H4 derived from the heterotetramer is buried due to hydrophobic stitching.