+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21157 | |||||||||
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Title | Yeast COMPASS in complex with a ubiquitinated nucleosome | |||||||||
Map data | Final, Sharpened map used for model building and refinement | |||||||||
Sample |
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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 / : / : / meiotic DNA double-strand break formation / ascospore formation ...: / positive regulation of synaptonemal complex assembly / : / : / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / : / : / meiotic DNA double-strand break formation / ascospore formation / sterol homeostasis / [histone H3]-lysine4 N-trimethyltransferase / regulation of chromatin organization / synaptonemal complex assembly / histone H3K4 trimethyltransferase activity / protein methylation / rDNA heterochromatin formation / protein-lysine N-methyltransferase activity / Set1C/COMPASS complex / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / methylated histone binding / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / telomere maintenance / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKBKE / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / 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 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of DVL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
Authors | Worden EJ / Wolberger C | |||||||||
Funding support | United States, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21157.map.gz | 228.3 MB | EMDB map data format | |
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Header (meta data) | emd-21157-v30.xml emd-21157.xml | 38.9 KB 38.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21157_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_21157.png | 165.1 KB | ||
Masks | emd_21157_msk_1.map | 244.1 MB | Mask map | |
Others | emd_21157_additional.map.gz emd_21157_half_map_1.map.gz emd_21157_half_map_2.map.gz | 193.1 MB 193.4 MB 193.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21157 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21157 | HTTPS FTP |
-Related structure data
Related structure data | 6venMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21157.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final, Sharpened map used for model building and refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21157_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Final, unsharpened map
File | emd_21157_additional.map | ||||||||||||
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Annotation | Final, unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_21157_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21157_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex between yeast COMPASS and a ubiquitinated Nucleosome
+Supramolecule #1: Complex between yeast COMPASS and a ubiquitinated Nucleosome
+Supramolecule #2: Yeast COMPASS
+Supramolecule #3: Ubiquitinated Nucleosome
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Ubiquitin
+Macromolecule #8: COMPASS component SWD3
+Macromolecule #9: COMPASS component SWD1
+Macromolecule #10: Histone-lysine N-methyltransferase, H3 lysine-4 specific
+Macromolecule #11: COMPASS component BRE2
+Macromolecule #12: COMPASS component SDC1
+Macromolecule #13: COMPASS component SPP1
+Macromolecule #5: 601 DNA (146-MER)
+Macromolecule #6: 601 DNA (146-MER)
+Macromolecule #14: ZINC ION
+Macromolecule #15: S-ADENOSYLMETHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 15 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: blot force 5 3.5 sec blot time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5784 / Average exposure time: 2.96 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |