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- PDB-6bx3: Structure of histone H3k4 methyltransferase -

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Basic information

Entry
Database: PDB / ID: 6bx3
TitleStructure of histone H3k4 methyltransferase
Components
  • (COMPASS component ...) x 5
  • Histone-lysine N-methyltransferase, H3 lysine-4 specific
KeywordsGENE REGULATION/Transferase / Histone H3K4 Methyltransferase / GENE REGULATION-Transferase complex
Function / homology
Function and homology information


regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / PKMTs methylate histone lysines / [histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / 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 / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / RMTs methylate histone arginines / subtelomeric heterochromatin formation / methylated histone binding / telomere maintenance / chromosome / histone binding / methylation / 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
Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Spp1/CFP1 ...Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Spp1/CFP1 / Histone-lysine N-methyltransferase Set1-like / : / Dpy-30 motif / Dpy-30 motif / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SWD3 / COMPASS component SWD1 / COMPASS component BRE2 / COMPASS component SPP1 / COMPASS component SDC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsSkiniotis, G. / Qu, Q.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)DK090165 United States
CitationJournal: Cell / Year: 2018
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
DepositionDec 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
E: Histone-lysine N-methyltransferase, H3 lysine-4 specific
K: COMPASS component BRE2
M: COMPASS component SDC1
N: COMPASS component SDC1
F: COMPASS component SPP1
B: COMPASS component SWD1
A: COMPASS component SWD3


Theoretical massNumber of molelcules
Total (without water)199,9837
Polymers199,9837
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific


Mass: 32162.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: SET1, SCY_2511 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A6ZT27, histone-lysine N-methyltransferase

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COMPASS component ... , 5 types, 6 molecules KMNFBA

#2: Protein COMPASS component BRE2 / Brefeldin-A sensitivity protein 2 / Complex proteins associated with SET1 protein BRE2 / Set1C component BRE2


Mass: 48306.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BRE2, CPS60, YLR015W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43132
#3: Protein/peptide COMPASS component SDC1 / Complex proteins associated with SET1 protein SDC1 / Set1C component SDC1 / Suppressor of CDC25 protein 1


Mass: 4810.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SDC1, CPS25, SAF19, YDR469W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03323
#4: Protein COMPASS component SPP1 / Complex proteins associated with SET1 protein SPP1 / Set1C component SPP1 / Suppressor of PRP protein 1


Mass: 28189.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPP1, CPS40, SAF41, YPL138C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03012
#5: Protein COMPASS component SWD1 / Complex proteins associated with SET1 protein SWD1 / Set1C component SWD1


Mass: 47047.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SWD1, CPS50, SAF49, YAR003W, FUN16 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P39706
#6: Protein COMPASS component SWD3 / Complex proteins associated with SET1 protein SWD3 / Set1C component SWD3


Mass: 34655.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SWD3, CPS30, SAF35, YBR175W, YBR1237 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P38123

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Multi-component complex of Set1 with its core subunits Cps25, Cps30, Cps40, Cps50 and Cps60
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 50000 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2UCSFImage4image acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIXdev-2880model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 163539
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163539 / Symmetry type: POINT

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