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- EMDB-20767: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-20767
TitleStructural basis of COMPASS eCM recognition of the H2Bub nucleosome
Map dataCOMPASS eCM/H2Bub nucleosome
Sample
  • Complex: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
    • Complex: nucleosome
      • Protein or peptide: x 6 types
      • DNA: x 2 types
    • Complex: COMPASS eCM
      • Protein or peptide: x 6 types
    • Complex: ubiquitin
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsComplex / methyltransferase / chromatin / epigenetics / TRANSFERASE-STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development ...[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / : / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / 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 / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / 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 / regulation of mitochondrial membrane potential / 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 / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB 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 / B30.2/SPRY domain profile. / 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. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / WD domain, G-beta repeat / 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. / 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 / Ubiquitin B / Histone H2B 1.1 / Polyubiquitin-B / Histone H4 / Histone H3.2 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-4 specific / KLLA0E24487p / KLLA0E03521p ...Histone H2B / Ubiquitin B / Histone H2B 1.1 / Polyubiquitin-B / Histone H4 / Histone H3.2 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-4 specific / KLLA0E24487p / KLLA0E03521p / KLLA0D07260p / KLLA0C10945p / KLLA0A08800p / Histone H3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHsu PL / Shi H
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol Cell / Year: 2019
Title: Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS.
Authors: Peter L Hsu / Hui Shi / Calvin Leonen / Jianming Kang / Champak Chatterjee / Ning Zheng /
Abstract: The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). ...The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well known as a prerequisite histone mark for COMPASS activity, how H2Bub activates COMPASS remains unclear. Here, we report the cryoelectron microscopy (cryo-EM) structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that autoinhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By delineating the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.
History
DepositionSep 26, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseNov 20, 2019-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uh5
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20767.png

Downloads & links

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Map

FileDownload / File: emd_20767.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOMPASS eCM/H2Bub nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 342.144 Å		1.06 Å/pix.
x 324 pix.
= 342.144 Å		1.06 Å/pix.
x 324 pix.
= 342.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.015
Minimum - Maximum-0.045239784 - 0.099906646
Average (Standard dev.)0.00028896317 (±0.0024564413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 342.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0561.0561.056
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z342.144342.144342.144
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0450.1000.000

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Supplemental data

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Sample components

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Entire : Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

EntireName: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
Components
  • Complex: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
    • Complex: nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H2B
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)
      • Protein or peptide: H3 N-terminus
    • Complex: COMPASS eCM
      • Protein or peptide: Swd3
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-4 specific
      • Protein or peptide: Swd1
      • Protein or peptide: Spp1
      • Protein or peptide: Bre2
      • Protein or peptide: Sdc1
    • Complex: ubiquitin
      • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

SupramoleculeName: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7, #12
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: COMPASS eCM

SupramoleculeName: COMPASS eCM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#10, #13-#15
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)

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Supramolecule #4: ubiquitin

SupramoleculeName: ubiquitin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #11
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.275879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CGIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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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 (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.69465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKAKTRSSRA GLQFPVGRVH RLLRKGNYAE RVGAGAPVYL AAVLEYLTAE ILELAGNAAR DNKKTRIIPR HLQLAVRNDE ELNKLLGRV TIAQGGVLPN IQSVLLPK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.82206 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT CYTSAK

UniProtKB: Histone H2B

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Macromolecule #8: Swd3

MacromoleculeName: Swd3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 36.458879 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MCDLDSVSDL TLTLRMLQFD KQVLPASGKI STSCQISPDG ELIAICQNTD MLVYEISSSK MMKLTTTHKE CINCLCWSPD SKCIASGSE DFTVEITHII YGRIRRLMGH TAPVISICYN NKGNILCSSS MDESIKEWHV LSGTALKTMS AHSDAVVSID I PKFDSSIL ...String:
MCDLDSVSDL TLTLRMLQFD KQVLPASGKI STSCQISPDG ELIAICQNTD MLVYEISSSK MMKLTTTHKE CINCLCWSPD SKCIASGSE DFTVEITHII YGRIRRLMGH TAPVISICYN NKGNILCSSS MDESIKEWHV LSGTALKTMS AHSDAVVSID I PKFDSSIL SSGSYDGLIR IFDTESGHCL KTLTYDKDWI AEDGVVPIST VKFSRNGKFL LVKSLDNVVK LWEYTRGTVV RT FLWPHQE TKAKLKYNCG LELIYPQGKD PLVISGNDSG SMCVWNVYSK NLVQKIDEKH RNSPLISISA SYDKVATLSL NGE CNLFRV H

UniProtKB: KLLA0E24487p

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Macromolecule #9: Histone-lysine N-methyltransferase, H3 lysine-4 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-4 specific
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 31.448504 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: YQQIEQNGII RDNQIALNEK EFDSTLASTT GSFIAEGFKK IPDKLKSSYL LHHRRLAQPL NTVHNHQEQN FMALNGTEST NQEADLEQD NHNASSRLNR VFQRRFQQDI EAQRAAIGFE SDLLSLNQLT KRKKPVTFAR SAIHNWGLYA LEPIAAKEMI I EYVGESIR ...String:
YQQIEQNGII RDNQIALNEK EFDSTLASTT GSFIAEGFKK IPDKLKSSYL LHHRRLAQPL NTVHNHQEQN FMALNGTEST NQEADLEQD NHNASSRLNR VFQRRFQQDI EAQRAAIGFE SDLLSLNQLT KRKKPVTFAR SAIHNWGLYA LEPIAAKEMI I EYVGESIR QPVAEMREKR YIKSGIGSSY LFRIDENTVI DATKRGGIAR FINHCCEPSC TAKIIKVDGR KRIVIYALRD IG TNEELTY DYKFERETDE GERLPCLCGA PSCKGFLN

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

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Macromolecule #10: Swd1

MacromoleculeName: Swd1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 49.894656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MANLLLQDPF GVLKEYPEKL THTLEVPVAA VCVKFSPRGD YLAVGCSNGA IIIYDMDSLK PIAMLGTHSG AHTRSVQSVC WSNDGRYLW SSGRDWYAKL WDMTQPTKCF QQYKFDGPLW SCHVVRWNVC IVTVVEEPTA YVLTLTDRQN AFHCFPLLEQ D QDISGHGY ...String:
MANLLLQDPF GVLKEYPEKL THTLEVPVAA VCVKFSPRGD YLAVGCSNGA IIIYDMDSLK PIAMLGTHSG AHTRSVQSVC WSNDGRYLW SSGRDWYAKL WDMTQPTKCF QQYKFDGPLW SCHVVRWNVC IVTVVEEPTA YVLTLTDRQN AFHCFPLLEQ D QDISGHGY TLVACPHPTI ESIIITGTSK GWINAFQLDL ESGFEDKIRC CYEEKIANAN IKQIIISPSG TRIAINGSDR TI RQYQLIV EDNESEGGSS HSVSIELEHK YQDIINRLQW NTIFFSNHSG EYLVASAHGS SAHDLYLWET SSGSLVRVLE GAD EELLDI DWNFYSMRIA SNGFESGWVY MWSIVIPPKW SALAPDFEEV EENIDYQEKE NEFDIMDDDN NLQAMTEAEE IAID LCTPE KYDVRGNDIS MPSFVIPIDY EGVIIQQHWA HQEQ

UniProtKB: KLLA0A08800p

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Macromolecule #11: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.622922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

UniProtKB: Ubiquitin B

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Macromolecule #12: H3 N-terminus

MacromoleculeName: H3 N-terminus / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 936.091 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTMQTAR

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Macromolecule #13: Spp1

MacromoleculeName: Spp1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 39.297867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLPSWCPRY DSRKHDPKTG EEVYCICKKP DTGELMVGCD GCDDWFHFSC LKIPEKYRDL VFSFYCSYCS AGITGPALIN GGKLPKTLW KRKCRLPECY TECDANSRSK YCSKKHAVQY VQSIVDKLNL PGVDKIALLR QLLNETTSLE EFKTLGRDKL P EVTSPLSK ...String:
MSLPSWCPRY DSRKHDPKTG EEVYCICKKP DTGELMVGCD GCDDWFHFSC LKIPEKYRDL VFSFYCSYCS AGITGPALIN GGKLPKTLW KRKCRLPECY TECDANSRSK YCSKKHAVQY VQSIVDKLNL PGVDKIALLR QLLNETTSLE EFKTLGRDKL P EVTSPLSK DQYSKLLEND QHLNKLINEH DELVSVKLSK LNEEDAVIEK YVNWIGEVNE RLSPHFNQPT GRKKSKSASK VT ICGYHNE FTIPRSVEEF LDKLLQLKED ENSNITSVDG VCVKTKCAKH QDWITLSQND LSEQKDSLEN VKRRLDLLIS VRT NQLRIS FFEQEMSNRV LPGVKT

UniProtKB: KLLA0D07260p

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Macromolecule #14: Bre2

MacromoleculeName: Bre2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 47.286996 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSVPVIPYLD YDIVDLGSDI KKPDFPQLSE SHRINEQQYY ITEDTPLNKR NFMYQPCAAN LMLDKLKYCG TDYFDKSSIN LMDRSDKLA FSLDDHSVSV SENCGWRSVR SDVCMKEGKI YWEVEVKNVS DTSHIRCGIS RREASTETPV GCDFYGYSIR D KGLQVIHE ...String:
MSVPVIPYLD YDIVDLGSDI KKPDFPQLSE SHRINEQQYY ITEDTPLNKR NFMYQPCAAN LMLDKLKYCG TDYFDKSSIN LMDRSDKLA FSLDDHSVSV SENCGWRSVR SDVCMKEGKI YWEVEVKNVS DTSHIRCGIS RREASTETPV GCDFYGYSIR D KGLQVIHE GRLHTVLKPH EMQAGDRIGF LLTLPSLQSQ SEQAMDYSLK RIQELNNDDS RTNKRNKKFN KEFYKFLLRS CE PTNVVRD QIAIRYKNQL FYESTDYVKT TKPEYYDNRD DMQKFYELEN SSFEVFVNGV SHGIAFEGLT PFLPPFSELQ YNE KFYLHH WNKRNVTKGI EIRNKYVNNN RLGYYATLSS FQGGTASIIT EAMELKFLPK DVDIKTLNDI YNEQIASDIV WDLI DEIDT

UniProtKB: KLLA0C10945p

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Macromolecule #15: Sdc1

MacromoleculeName: Sdc1 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 14.722625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSEPVMENMA PEDVVKLEKE EHIVPDIGVS SISTTEPLSP SGIPRESSGT VTSATAATTE REVSPKKELQ IDHDRVDPVA MIGGSTTRR YLNEHVTKHL LEGMKLIARE KPEDPLRVLG QFLIDASEMN QKPSS

UniProtKB: KLLA0E03521p

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Macromolecule #6: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 6 / 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 #7: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 7 / 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 #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #17: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 17 / 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

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215199
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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