+Open data
-Basic information
Entry | Database: PDB / ID: 6ven | ||||||
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Title | Yeast COMPASS in complex with a ubiquitinated nucleosome | ||||||
Components |
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Keywords | TRANSFERASE/STRUCTURAL PROTEIN/DNA / Methylation / histone / transcription / ubiquitin / gene regulation / TRANSFERASE-STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of synaptonemal complex assembly / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / ascospore formation / meiotic DNA double-strand break formation / sterol homeostasis / [histone H3]-lysine4 N-trimethyltransferase / regulation of chromatin organization / synaptonemal complex assembly ...positive regulation of synaptonemal complex assembly / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / ascospore formation / meiotic DNA double-strand break formation / sterol homeostasis / [histone H3]-lysine4 N-trimethyltransferase / regulation of chromatin organization / synaptonemal complex assembly / histone H3K4 trimethyltransferase activity / rDNA heterochromatin formation / protein methylation / protein-lysine N-methyltransferase activity / Set1C/COMPASS complex / RMTs methylate histone arginines / histone H3K4 methyltransferase activity / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / methylated histone binding / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / telomere maintenance / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) synthetic construct (others) Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
Authors | Worden, E.J. / Wolberger, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome. Authors: Evan J Worden / Xiangbin Zhang / Cynthia Wolberger / Abstract: 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 ...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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ven.cif.gz | 565.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ven.ent.gz | 443.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ven.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ven_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6ven_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6ven_validation.xml.gz | 82.6 KB | Display | |
Data in CIF | 6ven_validation.cif.gz | 126.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/6ven ftp://data.pdbj.org/pub/pdb/validation_reports/ve/6ven | HTTPS FTP |
-Related structure data
Related structure data | 21157MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 10 molecules AEBFCGDHKN
#1: Protein | Mass: 15251.830 Da / Num. of mol.: 2 / Mutation: K4(NLE), M90(NLE), M120(NLE), G102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pQE-81L / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G99R, A123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #4: Protein | Mass: 13498.715 Da / Num. of mol.: 2 / Mutation: K120C, S30T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P02281 #7: Protein | | Mass: 9036.393 Da / Num. of mol.: 1 / Mutation: G76C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48 #10: Protein | | Mass: 41508.488 Da / Num. of mol.: 1 / Fragment: UNP residues 762-1080 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SET1, KMT2, YTX1, YHR119W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi Five References: UniProt: P38827, [histone H3]-lysine4 N-trimethyltransferase |
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-601 DNA (146- ... , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44825.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#6: DNA chain | Mass: 45305.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-COMPASS component ... , 5 types, 6 molecules LMOPQR
#8: Protein | Mass: 34786.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SWD3, CPS30, SAF35, YBR175W, YBR1237 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P38123 | ||
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#9: Protein | Mass: 48702.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SWD1, CPS50, SAF49, YAR003W, FUN16 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P39706 | ||
#11: Protein | Mass: 58425.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BRE2, CPS60, YLR015W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P43132 | ||
#12: Protein | Mass: 19466.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SDC1, CPS25, SAF19, YDR469W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: Q03323 #13: Protein | | Mass: 45489.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPP1, CPS40, SAF41, YPL138C / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: Q03012 |
-Non-polymers , 2 types, 2 molecules
#14: Chemical | ChemComp-ZN / |
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#15: Chemical | ChemComp-SAM / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 5 3.5 sec blot time |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.96 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5784 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2036654 / Details: Relion template-based picking from 3D model | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 650847 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 110 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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