**3.2. The first crystal structure of a nucleosome-bound protein domain (RCC1)**

solved to date by crystallography and cryo-electron microscopy [39, 50–58]. The most recent addition to this ever-growing list is the spectacular structures of the complex between the INO80 chromatin remodeler and the nucleosome [59, 60]. Below, we discuss a few cardinal

The first high-resolution structure of a nucleosome-protein complex was the crystal structure of a peptide model of Kaposi's sarcoma-associated herpesvirus LANA N-terminal region bound to the nucleosome [61]. The binding site identified in this study was the acidic patch. The atomistic resolution allowed to identify intermolecular side chain interactions including the arginine anchor bound to the acidic triad. Ever since, the LANA-nucleosome has become a golden standard for comparisons with other acidic patch interactions [50, 55]. Importantly, LANA is used to investigate the acidic patch binding ability of other proteins by competitive binding [62–64]. Interestingly, this exact epitope happened to be the binding interface also for

**Name PDB-id Role Year Technique Reference Resolution [Å]**

2011, 2011, 2013, 2013

X-Ray [39, 51–53] 3.0 – 3.3

2017 X-Ray [78] 2.8

studies to highlight the different nucleosomal binding modes of effector proteins.

the first full protein domain that was crystalized in its nucleosome-bound state.

RCC1 3MVD Ran recruitment 2010 X-Ray [50] 2.9

CENP-C 4X23 H3 variant binding 2013 X-Ray [54] 3.5 Ring1B 4R8P E3 ligase 2014 X-Ray [55] 3.3 53BP1 5KGF Reader 2016 EM [40] 4.5 SAGA/DUB 4ZUX Eraser 2016 X-Ray [56] 3.8 Set8 5HQ2 Writer 2016 X-Ray [57] 4.5 Chd1 5O9G Remodeler 2017 X-Ray [74] 4.8 Snf2 5X0X, 5X0Y Remodeler 2017 EM [71] 4.0 CENP-N 6BUZ, 6C0W H3 variant binder 2017, 2018 EM [72, 73] 3.9/4.0 H1 4QLC, 5NL0 Linker histone 2015, 2017 X-Ray [45, 75] 3.5 INO80 6FML, 6ETX Remodeling complex 2018, 2018 EM [59, 60] 4.4/4.8

LANA 1ZLA, 5GTC Viral protein 2006, 2017 X-Ray [61, 76] 2.9/2.7 IE1 5E5A Viral protein 2016 X-Ray [77] 2.8

**Table 2.** Structures of nucleosome-protein or nucleosome-peptide complexes deposited in the RCSB protein databank

Chromatin compaction

**3.1. The first crystal structure of a nucleosome complex (LANA)**

**Proteins**

**Peptides**

PDB.

Sir3 BAH 4JJN, 3TU4,

26 Chromatin and Epigenetics

4LD9, 4KUD

GAG 5MLU Synthetic acetylation

system

The first structure of a protein bound to the nucleosome was the RCC1-nucleosome complex published by the Tan lab in 2010. RCC1 (regulator of chromosome condensation) is essential during mitosis by recruiting Ran GTPase, which plays a role in nucleus reorganization, to the nucleosome [65, 66]. A comparison with LANA highlighted the crucial and conserved interaction of arginine residues with the acidic patch triad [50]. Strikingly, RCC1 binds to the acidic patch using the canonical arginine anchor, here contained in a loop, and also binds the nucleosomal DNA through its N-terminal tail. Such synergetic interactions have been observed later in many other nucleosome-binding proteins [50, 55, 67–70]. This study was the first to show such complexity of nucleosomes as interaction platforms. It also highlights the importance of properly defining the boundaries of binding domains to capture all binding epitopes in order to reveal possible synergetic interactions and fully understand complex formation and subsequent effects on chromatin structure.
