Fig. 2: Crystal structure of an EPOP-bound PRC2.1 subcomplex.
From: EPOP restricts PRC2.1 targeting to chromatin by directly modulating enzyme complex dimerization
a Domain structures of the proteins captured in the crystal structure. Domain names are summarized below. SUZ12(N), N-terminal domain of SUZ12, contains ZnB, zinc finger-binding helix; WDB1, WD40-binding domain 1; C2, C2 domain; Zn, zinc finger domain; WDB2, WD40-binding domain 2. RBBP4 contains NT, N-terminal domain; WD40, WD40 domain. PHF19(RC), reversed chromodomain of PHF19. EPOP(C), C-terminal domain of EPOP. Subdomains or secondary structures of the PHF19(RC) and EPOP(C) are shown in brackets. (DS), dimer stabilization helix; (SC), short connecting helix; (C2B), C2-binding domain; (CT), C-terminal tail; (SH), short helix; (L1), loop 1; (βH), β hairpin; (L2), loop 2. The domain structures are color-coded based on proteins, except the DS helix of PHF19(RC), which is disordered in the structure and colored in gray. b 2FoFc electron density map of the EPOP fragment, contoured at 1.0σ, is shown in gray. The anomalous signal of the L325M mutant contoured at 10.0σ is shown in gold. c Sequence alignment of human EPOP, human SKDA1, and Drosophila Corto. Residues deleted in the EPOPD5 mutant are indicated by a dotted box. EPOP residues interacting with SUZ12 are indicated by blue discs, and proline residues contributing to the shape complementarity by blue squares. The secondary structure of the EPOP(C) is shown above the sequence alignment. d Cartoon representation of the overall structure. The SUZ12(N)–RBBP4–PHF19(RC)–EPOP(C) heterotetrameric complex adopts a dimeric structural architecture in the crystal lattice. Protein domains are labeled and color-coded. The two protomers are distinguished by the prime sign. e Overall structure in a different view with the rotation matrix relative to (d) indicated. f Close-up view of the EPOP binding interface. SUZ12 and RBBP4 domains are highlighted as transparent surfaces. Interacting residues are shown as sticks. Hydrogen bonds are indicated by black dotted lines. All proline residues from the EPOP fragment are also shown as sticks. g Structural alignment to PRC2.2. The current structure is aligned to a PRC2.2 subcomplex containing AEBP2 and JARID2 fragments (PDBs 5WAI and 6WKR). SUZ12 and RBBP4 are displayed as surfaces. Protein domains are labeled and color-coded. AEBP2 domains: C2B, C2-binding domain; CC, central connecting helix. JARID2 domain: TR, transrepression domain. Only the EPOP(C) domain from the current structure is shown for clarity. h Structural alignment to PRC2.1. The current structure is aligned to a PRC2.1 subcomplex containing the PHF19(RC) domain (PDB 6NQ3). SUZ12 and RBBP4 are displayed as surfaces. Protein domains are labeled and color-coded. Only one protomer of the dimer and the EPOP(C) domain from the current structure are shown for clarity. i Schematic model of the dimer disruption mechanism. The domain-swapped dimer is shown. The transient PRC2core dimer is locked by PHF19 in PRC2.1PHF19. EPOP unlocks the PRC2.1PHF19 dimer by partially displacing PHF19. The schematic is color-coded based on the crystal structures, with the gray disc representing PRC2 subunits and domains not involved in EPOP-mediated regulation.
