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- EMDB-43238: NPM2-H1.8 isolated from Xenopus egg extract -

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Basic information

Entry
Database: EMDB / ID: EMD-43238
TitleNPM2-H1.8 isolated from Xenopus egg extract
Map data
Sample
  • Cell: NPM2 complexed with H1.8
    • Protein or peptide: Nucleoplasmin isoform X1
KeywordsH1 / Xenopus egg extract / MagIC-cryo-EM / Histone chaperone / CHAPERONE
Function / homology
Function and homology information


single fertilization / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / nucleolus / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family
Similarity search - Domain/homology
Nucleoplasmin isoform X1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsArimura Y / Funabiki H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Elife / Year: 2025
Title: MagIC-Cryo-EM, structural determination on magnetic beads for scarce macromolecules in heterogeneous samples.
Authors: Yasuhiro Arimura / Hide A Konishi / Hironori Funabiki /
Abstract: Cryo-EM single-particle analyses typically require target macromolecule concentration at 0.05~5.0 mg/ml, which is often difficult to achieve. Here, we devise netic solation and oncentration (MagIC)- ...Cryo-EM single-particle analyses typically require target macromolecule concentration at 0.05~5.0 mg/ml, which is often difficult to achieve. Here, we devise netic solation and oncentration (MagIC)-cryo-EM, a technique enabling direct structural analysis of targets captured on magnetic beads, thereby reducing the targets' concentration requirement to <0.0005 mg/mL. Adapting MagIC-cryo-EM to a Chromatin Immunoprecipitation protocol, we characterized structural variations of the linker histone H1.8-associated nucleosomes that were isolated from interphase and metaphase chromosomes in egg extract. Combining plicated election o xclude ubbish particles (DuSTER), a particle curation method that excludes low signal-to-noise ratio particles, we also resolved the 3D cryo-EM structures of nucleoplasmin NPM2 co-isolated with the linker histone H1.8 and revealed distinct open and closed structural variants. Our study demonstrates the utility of MagIC-cryo-EM for structural analysis of scarce macromolecules in heterogeneous samples and provides structural insights into the cell cycle-regulation of H1.8 association to nucleosomes.
#1: Journal: Elife / Year: 2024
Title: MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples
Authors: Arimura Y / Konishi HA / Funabiki H
History
DepositionJan 2, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43238.png

Downloads & links

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Map

FileDownload / File: emd_43238.map.gz / Format: CCP4 / Size: 19.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 172 pix.
= 185.76 Å		1.08 Å/pix.
x 172 pix.
= 185.76 Å		1.08 Å/pix.
x 172 pix.
= 185.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.06731387 - 0.37438715
Average (Standard dev.)0.0006285855 (±0.012908843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions172172172
Spacing172172172
CellA=B=C: 185.76001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43238_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_43238_half_map_1.map
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Half map: #2

Fileemd_43238_half_map_2.map
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Sample components

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Entire : NPM2 complexed with H1.8

EntireName: NPM2 complexed with H1.8
Components
  • Cell: NPM2 complexed with H1.8
    • Protein or peptide: Nucleoplasmin isoform X1

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Supramolecule #1: NPM2 complexed with H1.8

SupramoleculeName: NPM2 complexed with H1.8 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Nucleoplasmin isoform X1

MacromoleculeName: Nucleoplasmin isoform X1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 21.949467 KDa
SequenceString: MASTVSNTSK LEKPVSLIWG CELNEQNKTF EFKVEDDEEK CEHQLALRTV CLGDKAKDEF HIVEIVTQEE GAEKSVPIAT LKPSILPMA TMVGIELTPP VTFRLKAGSG PLYISGQHVA MEEDYSWAEE EDEGEAEGEE EEEEEEDQES PPKAVKRPAA T KKAGQAKK ...String:
MASTVSNTSK LEKPVSLIWG CELNEQNKTF EFKVEDDEEK CEHQLALRTV CLGDKAKDEF HIVEIVTQEE GAEKSVPIAT LKPSILPMA TMVGIELTPP VTFRLKAGSG PLYISGQHVA MEEDYSWAEE EDEGEAEGEE EEEEEEDQES PPKAVKRPAA T KKAGQAKK KLDKEDESSE EDSPTKKGKG AGRGRKPAAK K

UniProtKB: Nucleoplasmin isoform X1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Details: 10mM HEPES-KOH (pH 7.4), 30 mM KCl, 1 mM EGTA, 10 ng/microL leupeptin, 10 ng/microL pepstatin, 10 ng/microL chymostatin, 1 mM sodium butyrate, 1 mM beta-glycerophosphate, trehalose, and 1,6-hexanediol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE
Details: The grid was incubated on the 40 x 20 mm N52 neodymium disc magnets for 5 minutes and vitrified using the Vitrobot Mark IV (FEI) with a 2-second blotting time at room temperature under 100% humidity conditions.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Average electron dose: 45.3 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 51.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 92428
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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