9B2S | pdb_00009b2s

Haspin bound to nucleosome in position 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Haspin kinase binds to a nucleosomal DNA supergroove.

Hicks, C.W.Gliech, C.R.Rahman, S.Zhang, X.Eneim, A.S.Vasquez, S.J.Holland, A.J.Wolberger, C.

(2025) Nat Struct Mol Biol 32: 1030-1037

  • DOI: https://doi.org/10.1038/s41594-025-01502-y
  • Primary Citation of Related Structures:  
    9B2S

  • PubMed Abstract: 

    Phosphorylation of histone H3 threonine 3 (H3T3) by Haspin recruits the chromosomal passenger complex to the inner centromere and ensures proper cell cycle progression through mitosis. The mechanism by which Haspin binds to nucleosomes to phosphorylate H3T3 is not known. Here we report cryogenic electron microscopy structures of the human Haspin kinase domain bound to a nucleosome. In contrast with previous structures of histone-modifying enzymes, Haspin solely contacts the nucleosomal DNA, inserting into a supergroove formed by apposing major grooves of two DNA gyres. This binding mode provides a plausible mechanism by which Haspin can bind to nucleosomes in a condensed chromatin environment to phosphorylate H3T3. We identify key basic residues in the Haspin kinase domain that are essential for phosphorylation of nucleosomal histone H3 and binding to mitotic chromatin. Our structural data provide notable insight into a histone-modifying enzyme that binds to nucleosomes solely through DNA contacts.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
136Xenopus laevisMutation(s): 1 
UniProt
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
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
123Xenopus laevisMutation(s): 1 
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Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase haspinI [auth K]357Homo sapiensMutation(s): 0 
Gene Names: HASPINGSG2
EC: 2.7.11.1
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Find proteins for Q8TF76 (Homo sapiens)
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PHAROS:  Q8TF76
GTEx:  ENSG00000177602 
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UniProt GroupQ8TF76
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Entity ID: 6
MoleculeChains LengthOrganismImage
601 DNA (185-MER)J [auth I]185synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
601 DNA (185-MER)K [auth J]185synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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 States5R35GM130393

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection
  • Version 1.2: 2025-08-06
    Changes: Data collection, Database references