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Open data
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Basic information
Entry | Database: PDB / ID: 6bx3 | ||||||
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Title | Structure of histone H3k4 methyltransferase | ||||||
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![]() | GENE REGULATION/Transferase / Histone H3K4 Methyltransferase / GENE REGULATION-Transferase complex | ||||||
Function / homology | ![]() regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / : / PKMTs methylate histone lysines / [histone H3]-lysine4 N-trimethyltransferase / Set1C/COMPASS complex / RMTs methylate histone arginines / subtelomeric heterochromatin formation / methylated histone binding / telomere maintenance ...regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / : / PKMTs methylate histone lysines / [histone H3]-lysine4 N-trimethyltransferase / Set1C/COMPASS complex / RMTs methylate histone arginines / subtelomeric heterochromatin formation / methylated histone binding / telomere maintenance / chromosome / histone binding / chromosome, telomeric region / transcription cis-regulatory region binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
![]() | Skiniotis, G. / Qu, Q.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex. Authors: Qianhui Qu / Yoh-Hei Takahashi / Yidai Yang / Hongli Hu / Yan Zhang / Joseph S Brunzelle / Jean-Francois Couture / Ali Shilatifard / Georgios Skiniotis / ![]() ![]() Abstract: The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity ...The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics. The Cps50 C-terminal tail weaves within the complex to provide a central scaffold for assembly. The SET domain, snugly positioned at the junction of the Y-shaped complex, is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). The mobile SET-I motif of the SET domain is engaged by Cps30, explaining its key role in COMPASS catalytic activity toward higher H3K4 methylation states. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.8 KB | Display | ![]() |
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PDB format | ![]() | 196.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1002.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 52.9 KB | Display | |
Data in CIF | ![]() | 78.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7303MC ![]() 6e29C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 32162.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: YJM789 / Gene: SET1, SCY_2511 / Production host: ![]() ![]() References: UniProt: A6ZT27, histone-lysine N-methyltransferase |
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-COMPASS component ... , 5 types, 6 molecules KMNFBA
#2: Protein | Mass: 48306.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BRE2, CPS60, YLR015W / Production host: ![]() ![]() | ||||||
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#3: Protein/peptide | Mass: 4810.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SDC1, CPS25, SAF19, YDR469W / Production host: ![]() ![]() #4: Protein | | Mass: 28189.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SPP1, CPS40, SAF41, YPL138C / Production host: ![]() ![]() #5: Protein | | Mass: 47047.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SWD1, CPS50, SAF49, YAR003W, FUN16 / Production host: ![]() ![]() #6: Protein | | Mass: 34655.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SWD3, CPS30, SAF35, YBR175W, YBR1237 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Multi-component complex of Set1 with its core subunits Cps25, Cps30, Cps40, Cps50 and Cps60 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.22 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: OTHER / Nominal magnification: 50000 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 163539 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163539 / Symmetry type: POINT |