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- EMDB-44115: Haspin bound to H3 tail -

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ID or keywords:

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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


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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / 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 / 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 / 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: To be published
Title: Haspin binds to nucleosomes using a unique DNA binding mechanism
Authors: Hicks CW / Gliech CR / Zhang X / Rahman S / Vasquez S / Holland AJ / Wolberger C
History
DepositionMar 16, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_44115_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_44115_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_44115_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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