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- EMDB-44115: Haspin bound to H3 tail -

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Basic information

Entry
Database: EMDB / ID: EMD-44115
TitleHaspin bound to H3 tail
Map datasharpened map
Sample
  • Complex: Haspin bound to H3 tail
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Serine/threonine-protein kinase haspin
Keywordshaspin / nucleosome / histone / chromatin / H3T3ph / DNA BINDING PROTEIN / DNA BINDING PROTEIN-Transferase complex
Function / homology
Function and homology information


histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / structural constituent of chromatin / nucleosome / mitotic cell cycle / chromosome / protein phosphorylation ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / structural constituent of chromatin / nucleosome / mitotic cell cycle / chromosome / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein heterodimerization activity / protein serine kinase activity / centrosome / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold ...Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Histone H3.2 / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsHicks CW / Wolberger C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM130393 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Haspin kinase binds to a nucleosomal DNA supergroove.
Authors: Chad W Hicks / Colin R Gliech / Sanim Rahman / Xiangbin Zhang / Andrew S Eneim / Stacy J Vasquez / Andrew J Holland / Cynthia Wolberger /
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 ...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.
History
DepositionMar 16, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44115.png

Downloads & links

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Map

FileDownload / File: emd_44115.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 400 pix.
= 388. Å		0.97 Å/pix.
x 400 pix.
= 388. Å		0.97 Å/pix.
x 400 pix.
= 388. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.097
Minimum - Maximum-0.98045254 - 1.2408757
Average (Standard dev.)-0.00028072268 (±0.010323248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 388.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44115_msk_1.map
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Additional map: unsharpened map

Fileemd_44115_additional_1.map
Annotationunsharpened map
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Half map: Half Map B

Fileemd_44115_half_map_1.map
AnnotationHalf Map B
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Half map: Half Map A

Fileemd_44115_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : Haspin bound to H3 tail

EntireName: Haspin bound to H3 tail
Components
  • Complex: Haspin bound to H3 tail
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Serine/threonine-protein kinase haspin

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Supramolecule #1: Haspin bound to H3 tail

SupramoleculeName: Haspin bound to H3 tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: This sample is a subcomponent of a larger sample of Haspin bound to nucleosome
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Serine/threonine-protein kinase haspin

MacromoleculeName: Serine/threonine-protein kinase haspin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.711484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSSG VDLGTENLYF QSMGECSQKG PVPFSHCLPT EKLQRCEKIG EGVFGEVFQT IADHTPVAIK IIAIEGPDLV NGSHQKTFE EILPEIIISK ELSLLSGEVC NRTEGFIGLN SVHCVQGSYP PLLLKAWDHY NSTKGSANDR PDFFKDDQLF I VLEFEFGG ...String:
MHHHHHHSSG VDLGTENLYF QSMGECSQKG PVPFSHCLPT EKLQRCEKIG EGVFGEVFQT IADHTPVAIK IIAIEGPDLV NGSHQKTFE EILPEIIISK ELSLLSGEVC NRTEGFIGLN SVHCVQGSYP PLLLKAWDHY NSTKGSANDR PDFFKDDQLF I VLEFEFGG IDLEQMRTKL SSLATAKSIL HQLTASLAVA EASLRFEHRD LHWGNVLLKK TSLKKLHYTL NGKSSTIPSC GL QVSIIDY TLSRLERDGI VVFCDVSMDE DLFTGDGDYQ FDIYRLMKKE NNNRWGEYHP YSNVLWLHYL TDKMLKQMTF KTK CNTPAM KQIKRKIQEF HRTMLNFSSA TDLLCQHSLF K

UniProtKB: Serine/threonine-protein kinase haspin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 481126
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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