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Structure paper

TitleStructural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif.
Journal, issue, pagesGenes Dev, Vol. 39, Issue 19-20, Page 1155-1161, Year 2025
Publish dateOct 1, 2025
AuthorsJaime Alegrio-Louro / Grisel Cruz-Becerra / George A Kassavetis / James T Kadonaga / Andres E Leschziner /
PubMed AbstractThe tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally ...The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally determined. Here we used cryo-EM to show that both proteins bind to the nucleosome acidic patch via analogous arginine anchors with one molecule bound to each face of the nucleosome. We additionally used the natural promoter-containing 5S rDNA sequence for structural analysis of the nucleosome. These structures of an ancient nucleosome-binding motif suggest that there is an untapped realm of proteins with a related mode of binding to chromatin.
External linksGenes Dev / PubMed:40721296 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.3 Å
Structure data

46536

9d3k

EMDB-46536, PDB-9d3k:
Two Dsup molecules in complex with the nucleosome open from both sides
Method: EM (single particle) / Resolution: 2.7 Å

46537

9d3l

EMDB-46537, PDB-9d3l:
Two Dsup molecules in complex with the nucleosome open from the left side
Method: EM (single particle) / Resolution: 2.8 Å

46538

9d3m

EMDB-46538, PDB-9d3m:
Two HMGN2s in complex with the nucleosome
Method: EM (single particle) / Resolution: 2.9 Å

46540

9d3n

EMDB-46540, PDB-9d3n:
167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde
Method: EM (single particle) / Resolution: 3.0 Å

46542

9d3o

EMDB-46542, PDB-9d3o:
167-bp 5S rDNA nucleosome - closed
Method: EM (single particle) / Resolution: 3.0 Å

46543

9d3p

EMDB-46543, PDB-9d3p:
167-bp 5S rDNA nucleosome - open I (open only on the downstream side)
Method: EM (single particle) / Resolution: 2.5 Å

46544

9d3q

EMDB-46544, PDB-9d3q:
167-bp 5S rDNA nucleosome - open II
Method: EM (single particle) / Resolution: 2.8 Å

46545

9d3r

EMDB-46545, PDB-9d3r:
147-bp 5S rDNA nucleosome - closed
Method: EM (single particle) / Resolution: 3.3 Å

46546

9d3s

EMDB-46546, PDB-9d3s:
147-bp 5S rDNA nucleosome - open I (open on the downstream side)
Method: EM (single particle) / Resolution: 3.1 Å

46547

9d3t

EMDB-46547, PDB-9d3t:
147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde
Method: EM (single particle) / Resolution: 2.8 Å

Source
  • xenopus borealis (Kenyan clawed frog)
  • synthetic construct (others)
  • homo sapiens (human)
  • ramazzottius varieornatus (invertebrata)
KeywordsGENE REGULATION/DNA / Dsup / nucleosome / tardigrade damage supressor protein / GENE REGULATION / GENE REGULATION-DNA complex / high mobility group N proteins (HMGN proteins) / HMGN2 / non-histone chromosomal proteins / 5S rDNA nucleosome / natural nucleosome positioning sequence / glutaraldehyde / cross-linking / DNA sequence-dependent breathing

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