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- PDB-6ugm: Structural basis of COMPASS eCM recognition of an unmodified nucl... -

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Basic information

Entry
Database: PDB / ID: 6ugm
TitleStructural basis of COMPASS eCM recognition of an unmodified nucleosome
Components
  • (DNA (146-MER)) x 2
  • Bre2
  • H3 N-terminus
  • Histone H2A
  • Histone H2B
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-4 specific
  • Sdc1
  • Spp1
  • Swd1
  • Swd3
KeywordsTRANSFERASE/STRUCTURAL PROTEIN/DNA / Complex / methyltransferase / epigenetics / chromatin / nucleosome / TRANSFERASE-STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / histone binding / methylation / transcription cis-regulatory region binding ...[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / histone binding / methylation / transcription cis-regulatory region binding / protein heterodimerization activity / DNA binding / RNA binding / nucleus / metal ion binding
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 / B30.2/SPRY domain / B30.2/SPRY 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 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 / Zinc finger, FYVE/PHD-type / Histone-fold / 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. / 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 / Histone H2B 1.1 / Histone H4 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-4 specific / KLLA0E24487p ...S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H2B 1.1 / Histone H4 / 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 (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHsu, P.L. / Shi, H. / Zheng, N.
Funding support United States, 2items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (146-MER)
J: DNA (146-MER)
K: Swd3
M: Histone-lysine N-methyltransferase, H3 lysine-4 specific
N: Swd1
R: H3 N-terminus
X: Spp1
L: Bre2
O: Sdc1
P: Sdc1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,24520
Polymers428,78118
Non-polymers4642
Water00
1


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

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Components

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Protein , 11 types, 15 molecules AEBFCGDHKMNXLOP

#1: Protein Histone H3


Mass: 15275.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h3g, H3l / Production host: Escherichia coli (E. coli) / References: UniProt: Q92133
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 11694.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B


Mass: 13848.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18032686mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L8FQ56, UniProt: P02281*PLUS
#5: Protein Histone H2B 1.1 / H2B1.1


Mass: 13834.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#8: Protein Swd3


Mass: 36458.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: KLLA0_E24487g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CLY5
#9: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SET1 / SET domain-containing protein 1


Mass: 31448.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: SET1, KLLA0F24134g / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6CIT4, histone-lysine N-methyltransferase
#10: Protein Swd1


Mass: 49894.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: KLLA0_A08800g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CXF3
#12: Protein Spp1


Mass: 39297.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: KLLA0_D07260g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CRQ4
#13: Protein Bre2


Mass: 47286.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: KLLA0_C10945g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CTQ1
#14: Protein Sdc1


Mass: 14722.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: KLLA0_E03521g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CPN6

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (146-MER)


Mass: 45114.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (146-MER)


Mass: 45305.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 1 types, 1 molecules R

#11: Protein/peptide H3 N-terminus


Mass: 378.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 2 molecules

#15: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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
1Yeast COMPASS eCM bound to an unmodified nucleosomeCOMPLEX#1-#140MULTIPLE SOURCES
2nucleosomeCOMPLEX#1-#7, #111RECOMBINANT
3COMPASS eCMCOMPLEX#8-#10, #12-#141RECOMBINANT
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Xenopus laevis (African clawed frog)8355
23Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)284590
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 74 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100905 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0124745
ELECTRON MICROSCOPYf_angle_d1.06734698
ELECTRON MICROSCOPYf_dihedral_angle_d18.27413874
ELECTRON MICROSCOPYf_chiral_restr0.0613908
ELECTRON MICROSCOPYf_plane_restr0.0083388

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