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- EMDB-7303: Structure of histone H3k4 methyltransferase -

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Basic information

Entry
Database: EMDB / ID: EMD-7303
TitleStructure of histone H3k4 methyltransferase
Map dataStructure of histone H3k4 methyltransferase
Sample
  • Complex: Multi-component complex of Set1 with its core subunits Cps25, Cps30, Cps40, Cps50 and Cps60
    • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-4 specificHistone methyltransferase
    • Protein or peptide: COMPASS component BRE2
    • Protein or peptide: COMPASS component SDC1
    • Protein or peptide: COMPASS component SPP1
    • Protein or peptide: COMPASS component SWD1
    • Protein or peptide: COMPASS component SWD3
KeywordsHistone 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 / : / [histone H3]-lysine4 N-trimethyltransferase / Set1C/COMPASS complex / subtelomeric heterochromatin formation / methylated histone binding / telomere maintenance / chromosome / histone binding ...regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / : / [histone H3]-lysine4 N-trimethyltransferase / Set1C/COMPASS complex / 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 / metal ion binding / nucleus / cytosol
Similarity search - Function
: / Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Spp1/CFP1 / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Dpy-30 motif ...: / Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Spp1/CFP1 / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / 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 / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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) / Saccharomyces cerevisiae (strain YJM789) (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsSkiniotis G / Qu QH
Funding support United States, 1 items
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, 2017-
Header (metadata) releaseJan 24, 2018-
Map releaseSep 5, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bx3
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7303.png

Downloads & links

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Map

FileDownload / File: emd_7303.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of histone H3k4 methyltransferase
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.35399103 - 0.9483957
Average (Standard dev.)0.0005927296 (±0.029994143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.3540.9480.001

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Supplemental data

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Sample components

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Entire : Multi-component complex of Set1 with its core subunits Cps25, Cps...

EntireName: Multi-component complex of Set1 with its core subunits Cps25, Cps30, Cps40, Cps50 and Cps60
Components
  • Complex: Multi-component complex of Set1 with its core subunits Cps25, Cps30, Cps40, Cps50 and Cps60
    • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-4 specificHistone methyltransferase
    • Protein or peptide: COMPASS component BRE2
    • Protein or peptide: COMPASS component SDC1
    • Protein or peptide: COMPASS component SPP1
    • Protein or peptide: COMPASS component SWD1
    • Protein or peptide: COMPASS component SWD3

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Supramolecule #1: Multi-component complex of Set1 with its core subunits Cps25, Cps...

SupramoleculeName: Multi-component complex of Set1 with its core subunits Cps25, Cps30, Cps40, Cps50 and Cps60
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 220 KDa

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

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-4 specific
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain YJM789) (yeast) / Strain: YJM789
Molecular weightTheoretical: 32.162402 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KIWQSRRKTL EEEKASDWQI ELNGTLFDSE LQPGSSFKAE GFRKVTDKLK INYLPHRRRV HQPLNTVNIH NERNEYTPEL CQREESSNK EPSDSVPQEV SSSRDNRASN RRFQQDIEAQ KAAIGTESEL LSLNQLNKRK KPVMFARSAI HNWGLYALDS I AAKEMIIE ...String:
KIWQSRRKTL EEEKASDWQI ELNGTLFDSE LQPGSSFKAE GFRKVTDKLK INYLPHRRRV HQPLNTVNIH NERNEYTPEL CQREESSNK EPSDSVPQEV SSSRDNRASN RRFQQDIEAQ KAAIGTESEL LSLNQLNKRK KPVMFARSAI HNWGLYALDS I AAKEMIIE YVGERIRQPV AEMREKRYLK NGIGSSYLFR VDENTVIDAT KKGGIARFIN HCCDPNCTAK IIKVGGRRRI VI YALRDIA ASEELTYDYK FEREKDDEER LPCLCGAPNC K

UniProtKB: Histone-lysine N-methyltransferase, H3 lysine-4 specific

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Macromolecule #2: COMPASS component BRE2

MacromoleculeName: COMPASS component BRE2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 48.306922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FDHSGMSVMD RSEGLSISRD GNDLVSVPDQ YGWRTARSDV CIKEGMTYWE VEVIRGGNKK FADGVNNKEN ADDSVDEVQS GIYEKMHKQ VNDTPHLRFG VCRREASLEA PVGFDVYGYG IRDISLESIH EGKLNCVLEN GSPLKEGDKI GFLLSLPSIH T QIKQAKEF ...String:
FDHSGMSVMD RSEGLSISRD GNDLVSVPDQ YGWRTARSDV CIKEGMTYWE VEVIRGGNKK FADGVNNKEN ADDSVDEVQS GIYEKMHKQ VNDTPHLRFG VCRREASLEA PVGFDVYGYG IRDISLESIH EGKLNCVLEN GSPLKEGDKI GFLLSLPSIH T QIKQAKEF TKRRIFALNS HMDTMNEPWR EDAENGPSRK KLKQETTNKE FQRALLEDIE YNDVVRDQIA IRYKNQLFFE AT DYVKTTK PEYYSSDKRE RQDYYQLEDS YLAIFQNGKY LGKAFENLKP LLPPFSELQY NEKFYLGYWQ HGEARDESND KNT TSAKKK KQQQKKKKGL ILRNKYVNNN KLGYYPTISC FNGGTARIIS EEDKLEYLDQ IRSAYCVDGN SKVNTLDTLY KEQI AEDIV WDIIDELEQI AL

UniProtKB: COMPASS component BRE2

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Macromolecule #3: COMPASS component SDC1

MacromoleculeName: COMPASS component SDC1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.810553 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
TRKYLNTNVT PHLLAGMRLI AVQQPEDPLR VLGEYLIEQS NI

UniProtKB: COMPASS component SDC1

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Macromolecule #4: COMPASS component SPP1

MacromoleculeName: COMPASS component SPP1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 28.189033 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HGREFVNDIW SRLKTDEDRA VVKKMVEQTG HIDKFKKFGQ LDFIDNNIVV KTDDEKEIFD QIVVRDMTLK TLEDDLQEVQ EISLPLFKK KLELLEVYLG WLDNVYTEMR KLDDDAASHV ECGKEDSKGT KRKKKKNSSR SRARKNICGY CSTYERIPCS V EEFVRDFG ...String:
HGREFVNDIW SRLKTDEDRA VVKKMVEQTG HIDKFKKFGQ LDFIDNNIVV KTDDEKEIFD QIVVRDMTLK TLEDDLQEVQ EISLPLFKK KLELLEVYLG WLDNVYTEMR KLDDDAASHV ECGKEDSKGT KRKKKKNSSR SRARKNICGY CSTYERIPCS V EEFVRDFG SNEEATKIHE VCTKWKCNRH LDWVSTNQEQ YLQQIDSLES MQERLQHLIQ ARKKQLNIQY YEEILRRGL

UniProtKB: COMPASS component SPP1

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Macromolecule #5: COMPASS component SWD1

MacromoleculeName: COMPASS component SWD1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 47.047637 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NILLQDPFAV LKEHPEKLTH TIENPLRTEC LQFSPCGDYL ALGCANGALV IYDMDTFRPI CVPGNMLGAH VRPITSIAWS PDGRLLLTS SRDWSIKLWD LSKPSKPLKE IRFDSPIWGC QWLDAKRRLC VATIFEESDA YVIDFSNDPV ASLLSKSDEK Q LSSTPDHG ...String:
NILLQDPFAV LKEHPEKLTH TIENPLRTEC LQFSPCGDYL ALGCANGALV IYDMDTFRPI CVPGNMLGAH VRPITSIAWS PDGRLLLTS SRDWSIKLWD LSKPSKPLKE IRFDSPIWGC QWLDAKRRLC VATIFEESDA YVIDFSNDPV ASLLSKSDEK Q LSSTPDHG YVLVCTVHTK HPNIIIVGTS KGWLDFYKFH SLYQTECIHS LKITSSNIKH LIVSQNGERL AINCSDRTIR QY EISIDDE NSAVELTLEH KYQDVINKLQ WNCILFSNNT AEYLVASTHG SSAHELYIWE TTSGTLVRVL EGAEEELIDI NWD FYSMSI VSNGFESGNV YVWSVVIPPK WSALAPDFEE VEENVDYLEK EDEFDEVDEA EQQQGLEQEE EIAIDLRTRE QYDV RGNNL LVERFTI

UniProtKB: COMPASS component SWD1

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Macromolecule #6: COMPASS component SWD3

MacromoleculeName: COMPASS component SWD3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 34.655438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FQFVTPVGTQ NGLKATCAKI SPDGQFLAIT QGLNILIYDI NRRTVSQTLV TSHARPFSEL CWSPDGQCIA TASDDFSVEI IHLSYGLLH TFIGHTAPVI SLTFNRKGNL LFTSSMDESI KIWDTLNGSL MKTISAHSEA VVSVDVPMND SSILSSGSYD G LIRIFDAE ...String:
FQFVTPVGTQ NGLKATCAKI SPDGQFLAIT QGLNILIYDI NRRTVSQTLV TSHARPFSEL CWSPDGQCIA TASDDFSVEI IHLSYGLLH TFIGHTAPVI SLTFNRKGNL LFTSSMDESI KIWDTLNGSL MKTISAHSEA VVSVDVPMND SSILSSGSYD G LIRIFDAE TGHCLKTLTY DKDWKRENGV VPISQVKFSE NARYLLVKSL DGVVKIWDCI GGCVVRTFQV QPLEKGVLHH SC GMDFLNP EDGSTPLVIS GYENGDIYCW NSDTKSLLQL LDGSLYHHSS PVMSIHCFGN IMCSLALNGD CCLWRWV

UniProtKB: COMPASS component SWD3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 9.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 163539
Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 163539
FSC plot (resolution estimation)

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