6S01

Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding.

Wang, H.Farnung, L.Dienemann, C.Cramer, P.

(2020) Nat Struct Mol Biol 27: 8-13

  • DOI: https://doi.org/10.1038/s41594-019-0345-4
  • Primary Citation of Related Structures:  
    6S01

  • PubMed Abstract: 

    Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified histone peptides, it is unclear how reader domains interact with modified nucleosomes. Here, we report the cryo-electron microscopy structure of the PWWP reader domain of human transcriptional coactivator LEDGF in complex with an H3K36-methylated nucleosome at 3.2-Å resolution. The structure reveals multivalent binding of the reader domain to the methylated histone tail and to both gyres of nucleosomal DNA, explaining the known cooperative interactions. The observed cross-gyre binding may contribute to nucleosome integrity during transcription. The structure also explains how human PWWP domain-containing proteins are recruited to H3K36-methylated regions of the genome for transcription, histone acetylation and methylation, and for DNA methylation and repair.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
135Xenopus laevisMutation(s): 1 
Gene Names: XELAEV_18002543mg
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Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PC4 and SFRS1-interacting protein530Homo sapiensMutation(s): 0 
Gene Names: PSIP1DFS70LEDGFPSIP2
UniProt & NIH Common Fund Data Resources
Find proteins for O75475 (Homo sapiens)
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PHAROS:  O75475
GTEx:  ENSG00000164985 
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UniProt GroupO75475
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Entity ID: 5
MoleculeChains LengthOrganismImage
Wisdom 601 DNA (165-MER)165synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
Wisdom 601 DNA (165-MER)165synthetic construct
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ML3
Query on ML3
A, E
L-PEPTIDE LINKINGC8 H19 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.5
MODEL REFINEMENTPHENIX1.14

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860, SPP1935
European Research CouncilGermany693023

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references