6UH5

Structural basis of COMPASS eCM recognition of the H2Bub nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS.

Hsu, P.L.Shi, H.Leonen, C.Kang, J.Chatterjee, C.Zheng, N.

(2019) Mol Cell 76: 712

  • DOI: 10.1016/j.molcel.2019.10.013
  • Primary Citation of Related Structures:  
    6UGM, 6UH5

  • PubMed 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). Although H2B monoubiquitination (H2Bub) is well known as a prerequisite histone mark for COMPASS activity, how H2Bub activates COMPASS remains unclear ...

    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.


    Organizational Affiliation

    Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address: nzheng@uw.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E135Xenopus laevisMutation(s): 0 
Gene Names: hist1h3gH3lh3c8.Sh3c8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G107Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mgh2ac14.Lh2ac14
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BD125Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BH125Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Swd3K327Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E24487g
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-4 specificL [auth M]275Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: SET1KLLA0F24134g
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Swd1M [auth N]439Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_A08800g
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinN [auth Q]76Homo sapiensMutation(s): 1 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
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PHAROS:  P0CG47
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
H3 N-terminusO [auth R]8Xenopus laevisMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Spp1P [auth X]342Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_D07260g
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Bre2Q [auth L]405Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_C10945g
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Sdc1R [auth O],
S [auth P]
134Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E03521g
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (146-MER)I 146synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (146-MER)J 146synthetic construct
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

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U [auth R]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
ZN
Query on ZN

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T [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Database references