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

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Basic information

Entry
Database: PDB / ID: 6ven
TitleYeast COMPASS in complex with a ubiquitinated nucleosome
Components
  • (601 DNA (146- ...) x 2
  • (COMPASS component ...) x 5
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-4 specificHistone methyltransferase
  • Ubiquitin
KeywordsTRANSFERASE/STRUCTURAL PROTEIN/DNA / Methylation / 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 / ascospore formation / sterol homeostasis / [histone H3]-lysine4 N-trimethyltransferase / regulation of chromatin organization / synaptonemal complex assembly ...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 / ascospore formation / sterol homeostasis / [histone H3]-lysine4 N-trimethyltransferase / regulation of chromatin organization / synaptonemal complex assembly / histone H3K4 trimethyltransferase activity / rDNA heterochromatin formation / protein methylation / protein-lysine N-methyltransferase activity / Set1C/COMPASS complex / histone H3K4 methyltransferase activity / silent mating-type cassette heterochromatin formation / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / methylated histone binding / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / telomere maintenance / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / 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 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import
Similarity search - Function
: / Histone-lysine N-methyltransferase, RNA-binding domain / 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. / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / Spp1/CFP1 / COMPASS (Complex proteins associated with Set1p) component N ...: / Histone-lysine N-methyltransferase, RNA-binding domain / 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. / Histone-lysine N-methyltransferase Set1-like / 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. / Histone, subunit A / Histone, subunit A / 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 superfamily / SET domain / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Zinc finger, FYVE/PHD-type / 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. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / COMPASS component SWD3 / Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SWD1 ...S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / DNA (> 100) / 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 speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Homo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWorden, E.J. / Wolberger, C.
Funding support United States, 1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: 601 DNA (146-MER)
J: 601 DNA (146-MER)
K: Ubiquitin
L: COMPASS component SWD3
M: COMPASS component SWD1
N: Histone-lysine N-methyltransferase, H3 lysine-4 specific
O: COMPASS component BRE2
P: COMPASS component SDC1
Q: COMPASS component SDC1
R: COMPASS component SPP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,46120
Polymers474,99718
Non-polymers4642
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, native gel electrophoresis, microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area77610 Å2
ΔGint-490 kcal/mol
Surface area143450 Å2

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Components

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Protein , 6 types, 10 molecules AEBFCGDHKN

#1: Protein Histone H3.2


Mass: 15251.830 Da / Num. of mol.: 2 / Mutation: K4(NLE), M90(NLE), M120(NLE), G102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pQE-81L / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P84233
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G99R, A123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13498.715 Da / Num. of mol.: 2 / Mutation: K120C, S30T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P02281
#7: Protein Ubiquitin /


Mass: 9036.393 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#10: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific / Histone methyltransferase / COMPASS component SET1 / Lysine N-methyltransferase 2 / SET domain-containing protein 1


Mass: 41508.488 Da / Num. of mol.: 1 / Fragment: UNP residues 762-1080
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SET1, KMT2, YTX1, YHR119W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi Five
References: UniProt: P38827, [histone H3]-lysine4 N-trimethyltransferase

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601 DNA (146- ... , 2 types, 2 molecules IJ

#5: DNA chain 601 DNA (146-MER)


Mass: 44825.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain 601 DNA (146-MER)


Mass: 45305.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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

#8: Protein COMPASS component SWD3 / Complex proteins associated with SET1 protein SWD3 / Set1C component SWD3


Mass: 34786.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWD3, CPS30, SAF35, YBR175W, YBR1237 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P38123
#9: Protein COMPASS component SWD1 / Complex proteins associated with SET1 protein SWD1 / Set1C component SWD1


Mass: 48702.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWD1, CPS50, SAF49, YAR003W, FUN16 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P39706
#11: Protein COMPASS component BRE2 / Brefeldin-A sensitivity protein 2 / Complex proteins associated with SET1 protein BRE2 / Set1C component BRE2


Mass: 58425.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRE2, CPS60, YLR015W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: P43132
#12: Protein COMPASS component SDC1 / Complex proteins associated with SET1 protein SDC1 / Set1C component SDC1 / Suppressor of CDC25 protein 1


Mass: 19466.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SDC1, CPS25, SAF19, YDR469W / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: Q03323
#13: Protein COMPASS component SPP1 / Complex proteins associated with SET1 protein SPP1 / Set1C component SPP1 / Suppressor of PRP protein 1


Mass: 45489.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPP1, CPS40, SAF41, YPL138C / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi five / References: UniProt: Q03012

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Non-polymers , 2 types, 2 molecules

#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex between yeast COMPASS and a ubiquitinated NucleosomeCOMPLEX#1-#130MULTIPLE SOURCES
2Yeast COMPASSCOMPLEX#8-#131RECOMBINANT
3Ubiquitinated NucleosomeCOMPLEX#1-#71RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (brewer's yeast)4932
23Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
12Trichoplusia ni (cabbage looper)7111Hi FiveBacmid
23Escherichia coli (E. coli)562plasmid
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMTris1
2100 mMSodium ChlorideNaClSodium chloride1
32 mMDTT1
425 uMS-adenosyl methionine1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 5 3.5 sec blot time

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.96 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5784
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
4CTFFINDCTF correction
7UCSF Chimera1.13.1model fitting
8Coot0.8.9.1model fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2036654 / Details: Relion template-based picking from 3D model
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 650847 / Symmetry type: POINT
Atomic model buildingB value: 110 / Protocol: OTHER / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
16CHG

6chg

1
26BX3

6bx3

F1
36BX3

6bx3

E1799-850
46NJ9

6nj9

1

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