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- EMDB-21157: Yeast COMPASS in complex with a ubiquitinated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-21157
TitleYeast COMPASS in complex with a ubiquitinated nucleosome
Map dataFinal, Sharpened map used for model building and refinement
Sample
  • Complex: Complex between yeast COMPASS and a ubiquitinated Nucleosome
    • Complex: Yeast COMPASS
      • Protein or peptide: x 6 types
    • Complex: Ubiquitinated Nucleosome
      • Protein or peptide: x 5 types
      • DNA: x 2 types
  • Ligand: x 2 types
KeywordsMethylation / 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 / meiotic DNA double-strand break formation / sterol homeostasis / ascospore formation / [histone H3]-lysine4 N-trimethyltransferase / synaptonemal complex assembly / regulation of chromatin organization ...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 / meiotic DNA double-strand break formation / sterol homeostasis / ascospore formation / [histone H3]-lysine4 N-trimethyltransferase / synaptonemal complex assembly / regulation of chromatin organization / histone H3K4 trimethyltransferase activity / protein methylation / rDNA heterochromatin formation / Set1C/COMPASS complex / protein-lysine N-methyltransferase activity / RMTs methylate histone arginines / histone H3K4 methyltransferase activity / silent mating-type cassette heterochromatin formation / cellular response to stress / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / telomere maintenance / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling
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 / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N ...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 / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Spp1/CFP1 / : / 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 / SET domain / SET domain superfamily / SET domain profile. / SET domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / : / Histone H2B signature. / Histone H2B / Histone H2B / Zinc finger PHD-type profile. / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Zinc finger, PHD-finger / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Ubiquitin conserved site / Core histone H2A/H2B/H3/H4 / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / COMPASS component SWD3 / Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SWD1 / COMPASS component BRE2 / Histone H4 / Histone H3.2 / COMPASS component SPP1 / COMPASS component SDC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWorden EJ / Wolberger C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130393 United States
CitationJournal: 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
DepositionJan 2, 2020-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0128
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0128
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ven
  • Surface level: 0.0128
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21157.png

Downloads & links

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Map

FileDownload / File: emd_21157.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal, Sharpened map used for model building and refinement
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0128 / Movie #1: 0.0128
Minimum - Maximum-0.05549551 - 0.10393735
Average (Standard dev.)-0.0000038609714 (±0.0020548622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0550.104-0.000

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Supplemental data

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Mask #1

Fileemd_21157_msk_1.map
Projections & Slices
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Additional map: Final, unsharpened map

Fileemd_21157_additional.map
AnnotationFinal, unsharpened map
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AxesZYX

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Half map: #1

Fileemd_21157_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_21157_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex between yeast COMPASS and a ubiquitinated Nucleosome

EntireName: Complex between yeast COMPASS and a ubiquitinated Nucleosome
Components
  • Complex: Complex between yeast COMPASS and a ubiquitinated Nucleosome
    • Complex: Yeast COMPASS
      • Protein or peptide: COMPASS component SWD3
      • Protein or peptide: COMPASS component SWD1
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-4 specific
      • Protein or peptide: COMPASS component BRE2
      • Protein or peptide: COMPASS component SDC1
      • Protein or peptide: COMPASS component SPP1
    • Complex: Ubiquitinated Nucleosome
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
      • DNA: 601 DNA (146-MER)
      • DNA: 601 DNA (146-MER)
      • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Complex between yeast COMPASS and a ubiquitinated Nucleosome

SupramoleculeName: Complex between yeast COMPASS and a ubiquitinated Nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13

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Supramolecule #2: Yeast COMPASS

SupramoleculeName: Yeast COMPASS / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #8-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Ubiquitinated Nucleosome

SupramoleculeName: Ubiquitinated Nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#7
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.25183 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ART(NLE)QTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV (NLE)ALQEASEAY LVALFEDTNL CAIHAKRVTI (NLE)PKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.498715 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTCYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.036393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGC

UniProtKB: Polyubiquitin-C

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Macromolecule #8: COMPASS component SWD3

MacromoleculeName: COMPASS component SWD3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.786637 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MFQFVTPVGT QNGLKATCAK ISPDGQFLAI TQGLNILIYD INRRTVSQTL VTSHARPFSE LCWSPDGQCI ATASDDFSVE IIHLSYGLL HTFIGHTAPV ISLTFNRKGN LLFTSSMDES IKIWDTLNGS LMKTISAHSE AVVSVDVPMN DSSILSSGSY D GLIRIFDA ...String:
MFQFVTPVGT QNGLKATCAK ISPDGQFLAI TQGLNILIYD INRRTVSQTL VTSHARPFSE LCWSPDGQCI ATASDDFSVE IIHLSYGLL HTFIGHTAPV ISLTFNRKGN LLFTSSMDES IKIWDTLNGS LMKTISAHSE AVVSVDVPMN DSSILSSGSY D GLIRIFDA ETGHCLKTLT YDKDWKRENG VVPISQVKFS ENARYLLVKS LDGVVKIWDC IGGCVVRTFQ VQPLEKGVLH HS CGMDFLN PEDGSTPLVI SGYENGDIYC WNSDTKSLLQ LLDGSLYHHS SPVMSIHCFG NIMCSLALNG DCCLWRWV

UniProtKB: COMPASS component SWD3

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Macromolecule #9: COMPASS component SWD1

MacromoleculeName: COMPASS component SWD1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.702574 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNILLQDPFA VLKEHPEKLT HTIENPLRTE CLQFSPCGDY LALGCANGAL VIYDMDTFRP ICVPGNMLGA HVRPITSIAW SPDGRLLLT SSRDWSIKLW DLSKPSKPLK EIRFDSPIWG CQWLDAKRRL CVATIFEESD AYVIDFSNDP VASLLSKSDE K QLSSTPDH ...String:
MNILLQDPFA VLKEHPEKLT HTIENPLRTE CLQFSPCGDY LALGCANGAL VIYDMDTFRP ICVPGNMLGA HVRPITSIAW SPDGRLLLT SSRDWSIKLW DLSKPSKPLK EIRFDSPIWG CQWLDAKRRL CVATIFEESD AYVIDFSNDP VASLLSKSDE K QLSSTPDH GYVLVCTVHT KHPNIIIVGT SKGWLDFYKF HSLYQTECIH SLKITSSNIK HLIVSQNGER LAINCSDRTI RQ YEISIDD ENSAVELTLE HKYQDVINKL QWNCILFSNN TAEYLVASTH GSSAHELYIW ETTSGTLVRV LEGAEEELID INW DFYSMS IVSNGFESGN VYVWSVVIPP KWSALAPDFE EVEENVDYLE KEDEFDEVDE AEQQQGLEQE EEIAIDLRTR EQYD VRGNN LLVERFTIPT DYTRIIKMQS S

UniProtKB: COMPASS component SWD1

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Macromolecule #10: Histone-lysine N-methyltransferase, H3 lysine-4 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-4 specific
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine4 N-trimethyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 41.508488 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGSS DYKDHDGDYK DHDIDYKDDD DKENLYFQGM DLQNAIKDEE DMLILKQLLS TYTPTVTPET SAALEYKIWQ SRRKVLEEE KASDWQIELN GTLFDSELQP GSSFKAEGFR KIADKLKINY LPHRRRVHQP LNTVNIHNER NEYTPELCQR E ESSNKEPS ...String:
MHHHHHHGSS DYKDHDGDYK DHDIDYKDDD DKENLYFQGM DLQNAIKDEE DMLILKQLLS TYTPTVTPET SAALEYKIWQ SRRKVLEEE KASDWQIELN GTLFDSELQP GSSFKAEGFR KIADKLKINY LPHRRRVHQP LNTVNIHNER NEYTPELCQR E ESSNKEPS DSVPQEVSSS RDNRASNRRF QQDIEAQKAA IGTESELLSL NQLNKRKKPV MFARSAIHNW GLYALDSIAA KE MIIEYVG ERIRQPVAEM REKRYLKNGI GSSYLFRVDE NTVIDATKKG GIARFINHCC DPNCTAKIIK VGGRRRIVIY ALR DIAASE ELTYDYKFER EKDDEERLPC LCGAPNCKGF LN

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

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Macromolecule #11: COMPASS component BRE2

MacromoleculeName: COMPASS component BRE2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 58.425301 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKLGIIPYQE GTDIVYKNAL QGQQEGKRPN LPQMEATHQI KSSVQGTSYE FVRTEDIPLN RRHFVYRPCS ANPFFTILGY GCTEYPFDH SGMSVMDRSE GLSISRDGND LVSVPDQYGW RTARSDVCIK EGMTYWEVEV IRGGNKKFAD GVNNKENADD S VDEVQSGI ...String:
MKLGIIPYQE GTDIVYKNAL QGQQEGKRPN LPQMEATHQI KSSVQGTSYE FVRTEDIPLN RRHFVYRPCS ANPFFTILGY GCTEYPFDH SGMSVMDRSE GLSISRDGND LVSVPDQYGW RTARSDVCIK EGMTYWEVEV IRGGNKKFAD GVNNKENADD S VDEVQSGI YEKMHKQVND TPHLRFGVCR REASLEAPVG FDVYGYGIRD ISLESIHEGK LNCVLENGSP LKEGDKIGFL LS LPSIHTQ IKQAKEFTKR RIFALNSHMD TMNEPWREDA ENGPSRKKLK QETTNKEFQR ALLEDIEYND VVRDQIAIRY KNQ LFFEAT DYVKTTKPEY YSSDKRERQD YYQLEDSYLA IFQNGKYLGK AFENLKPLLP PFSELQYNEK FYLGYWQHGE ARDE SNDKN TTSAKKKKQQ QKKKKGLILR NKYVNNNKLG YYPTISCFNG GTARIISEED KLEYLDQIRS AYCVDGNSKV NTLDT LYKE QIAEDIVWDI IDELEQIALQ Q

UniProtKB: COMPASS component BRE2

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Macromolecule #12: COMPASS component SDC1

MacromoleculeName: COMPASS component SDC1 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.466219 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MNESENSPQH NEVTVPMVED TSSNADIPME QIQREDNKNY DKHDNECFDM NGNHNNNSDN LQFDSVPSSA TKDLKNIKSV TNQNVKIEE SSSTNSVIEE SSEPKISKLE NVNLAATVGG SQTRKYLNTN VTPHLLAGMR LIAVQQPEDP LRVLGEYLIE Q SNILKSGE KESNASK

UniProtKB: COMPASS component SDC1

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Macromolecule #13: COMPASS component SPP1

MacromoleculeName: COMPASS component SPP1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.489457 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK GSENLYFQGS LPQWCPPHST LKRNPTTGED VYCICKRPDY GELMVGCDGC DDWFHFTCL HIPEQFKDLV FSFYCPYCQA GITGKNKDAI INGEGSLPKT LWKRKCRISD CYKPCLQDSK YCSEEHGREF V NDIWSRLK ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK GSENLYFQGS LPQWCPPHST LKRNPTTGED VYCICKRPDY GELMVGCDGC DDWFHFTCL HIPEQFKDLV FSFYCPYCQA GITGKNKDAI INGEGSLPKT LWKRKCRISD CYKPCLQDSK YCSEEHGREF V NDIWSRLK TDEDRAVVKK MVEQTGHIDK FKKFGQLDFI DNNIVVKTDD EKEIFDQIVV RDMTLKTLED DLQEVQEISL PL FKKKLEL LEVYLGWLDN VYTEMRKLDD DAASHVECGK EDSKGTKRKK KKNSSRSRAR KNICGYCSTY ERIPCSVEEF VRD FGSNEE ATKIHEVCTK WKCNRHLDWV STNQEQYLQQ IDSLESMQER LQHLIQARKK QLNIQYYEEI LRRGL

UniProtKB: COMPASS component SPP1

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Macromolecule #5: 601 DNA (146-MER)

MacromoleculeName: 601 DNA (146-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.825559 KDa
SequenceString: (DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DC) (DG)(DA)(DT)

+
Macromolecule #6: 601 DNA (146-MER)

MacromoleculeName: 601 DNA (146-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.305852 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DG)(DA)

+
Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #15: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 15 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
30.0 mMTris
100.0 mMSodium ChlorideNaCl
2.0 mMDTT
25.0 uMS-adenosyl methionine
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: blot force 5 3.5 sec blot time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2036654 / Details: Relion template-based picking from 3D model
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bx3


Details: Also used 1KX3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 650847
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6chg

source_name: PDB, initial_model_type: experimental model

6bx3

chain_id: F, source_name: PDB, initial_model_type: experimental model

6bx3

chain_id: E, residue_range: 799-850, source_name: PDB, initial_model_type: experimental model

6nj9

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 110
Output model

PDB-6ven:
Yeast COMPASS in complex with a ubiquitinated nucleosome

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