6ven | pdb_00006ven

Yeast COMPASS in complex with a ubiquitinated nucleosome

spinqualitylabelsall models 6ven, resolution 3.37Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ven is a 18 chain structure with sequence from [1], Atcc 18824, African clawed frog and Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: SAM, ZN NonStd Res: NLE Gene: SET1, KMT2, YTX1, YHR119W (ATCC 18824), BRE2, CPS60, YLR015W (ATCC 18824), SDC1, CPS25, SAF19, YDR469W (ATCC 18824), SPP1, CPS40, SAF41, YPL138C (ATCC 18824), UBC (HUMAN), SWD3, CPS30, SAF35, YBR175W, YBR1237 (ATCC 18824), SWD1, CPS50, SAF49, YAR003W, FUN16 (ATCC 18824) Activity: [Histone_H3-lysine(4)_N-trimethyltransferase [Histone H3]-lysine(4) N-trimethyltransferase], with EC number 2.1.1.354 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [BRE2_YEAST] The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. [H2A1_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [UBC_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling. [SWD1_YEAST] The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. [SDC1_YEAST] The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently activates gene expression by regulating transcription elongation and plays a role in telomere length maintenance. [H4_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [SWD3_YEAST] The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. [H32_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [H2B11_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [SPP1_YEAST] The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. [SET1_YEAST] Catalytic component of the COMPASS (Set1C) complex that specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. Publication Abstract from PubMed Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxxxRR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation. Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome.,Worden EJ, Zhang X, Wolberger C Elife. 2020 Jan 10;9. pii: 53199. doi: 10.7554/eLife.53199. PMID:31922488 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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