4NFT

Crystal structure of human lnkH2B-h2A.Z-Anp32e

Summary for 4NFT

• Entry DOI: 10.2210/pdb4nft/pdb
• Descriptor: Histone H2B type 2-E, Histone H2A.Z, Acidic leucine-rich nuclear phosphoprotein 32 family member E (3 entities in total)
• Functional Keywords: histone binding protein, chaperone
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P0C0S5; Cytoplasm : Q9BTT0
• Total number of polymer chains: 6
• Total formula weight: 102091.10

Authors

Shan, S.,Pan, L.,Mao, Z.,Wang, W.,Sun, J.,Dong, Q.,Liang, X.,Ding, X.,Chen, S.,Dai, L.,Zhang, Z.,Zhu, B.,Zhou, Z. (deposition date: 2013-11-01, release date: 2014-04-09, Last modification date: 2024-03-20)

Primary citation

Mao, Z.,Pan, L.,Wang, W.,Sun, J.,Shan, S.,Dong, Q.,Liang, X.,Dai, L.,Ding, X.,Chen, S.,Zhang, Z.,Zhu, B.,Zhou, Z.
Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z
Cell Res., 24:389-399, 2014

PubMed Abstract: H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is preferentially recognized by non-histone proteins remains elusive. Here we identified Anp32e, a novel higher eukaryote-specific histone chaperone for H2A.Z. Anp32e preferentially associates with H2A.Z-H2B dimers rather than H2A-H2B dimers in vitro and in vivo and dissociates non-nucleosomal aggregates formed by DNA and H2A-H2B. We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change. Genome-wide profiling of Anp32e revealed a remarkable co-occupancy between Anp32e and H2A.Z. Cells overexpressing Anp32e displayed a strong global H2A.Z loss at the +1 nucleosomes, whereas cells depleted of Anp32e displayed a moderate global H2A.Z increase at the +1 nucleosomes. This suggests that Anp32e may help to resolve the non-nucleosomal H2A.Z aggregates and also facilitate the removal of H2A.Z at the +1 nucleosomes, and the latter may help RNA polymerase II to pass the first nucleosomal barrier.

PubMed: 24613878
DOI: 10.1038/cr.2014.30

Experimental method

X-RAY DIFFRACTION (2.61 Å)