6VEN

Yeast COMPASS in complex with a ubiquitinated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome.

Worden, E.J.Zhang, X.Wolberger, C.

(2020) Elife 9

  • DOI: 10.7554/eLife.53199
  • Structures With Same Primary Citation

  • PubMed 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 methyltransferase subunit of COMPASS. We report here the cryo-EM ...

    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.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2A, E135Xenopus laevisMutation(s): 4 
Find proteins for P84233 (Xenopus laevis)
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4B, F102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1C, G129Xenopus laevisMutation(s): 2 
Find proteins for P06897 (Xenopus laevis)
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1D, H122Xenopus laevisMutation(s): 2 
Find proteins for P02281 (Xenopus laevis)
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
UbiquitinK80Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P0CG48
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  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SWD3L315Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SWD3CPS30SAF35YBR175WYBR1237
Find proteins for P38123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SWD1M426Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SWD1CPS50SAF49YAR003WFUN16
Find proteins for P39706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-4 specificN358Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SET1KMT2YTX1YHR119W
EC: 2.1.1.354
Find proteins for P38827 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
COMPASS component BRE2O505Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BRE2CPS60YLR015W
Find proteins for P43132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SDC1P, Q175Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SDC1CPS25SAF19YDR469W
Find proteins for Q03323 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SPP1R391Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPP1CPS40SAF41YPL138C
Find proteins for Q03012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
601 DNA (146-MER)I146synthetic construct

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Entity ID: 6
MoleculeChainsLengthOrganism
601 DNA (146-MER)J146synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

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N
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
ZN
Query on ZN

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N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
A,EL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM130393

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references