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

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 4 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
129Xenopus laevisMutation(s): 2 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 2 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
K
80Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SWD3
L
315Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SWD3 (CPS30, SAF35)
Find proteins for P38123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38123
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SWD1
M
426Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SWD1 (CPS50, SAF49)
Find proteins for P39706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39706
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-4 specific
N
358Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SET1 (KMT2, YTX1)
EC: 2.1.1.354
Find proteins for P38827 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38827
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
COMPASS component BRE2
O
505Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BRE2 (CPS60)
Find proteins for P43132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43132
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SDC1
P, Q
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SDC1 (CPS25, SAF19)
Find proteins for Q03323 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SDC1
Go to UniProtKB:  Q03323
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SPP1
R
391Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPP1 (CPS40, SAF41)
Find proteins for Q03012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SPP1
Go to UniProtKB:  Q03012
Entity ID: 5
MoleculeChainsLengthOrganism
601 DNA (146-MER)I146synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
601 DNA (146-MER)J146synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
N
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
A, E
L-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

View Full Validation Report or Ramachandran Plots



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
    Type: Database references