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- EMDB-2866: Reconstruction of nucleoplasmin isolated from egg -

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Basic information

Entry
Database: EMDB / ID: EMD-2866
TitleReconstruction of nucleoplasmin isolated from egg
Map datareconstruction of egg nucleoplasmin
Sample
  • Sample: reconstruction of egg Nucleoplasmin
  • Protein or peptide: nucleoplasmin
KeywordsNucleoplasmin / Histone-binding / post-translation modification
Biological speciesXenopus (frog)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å
AuthorsOnikubo T / Nicklay JJ / Xing L / Warren C / Anson B / Wang WL / Burgos ES / Ruff SE / Shabanowitz J / Cheng RH ...Onikubo T / Nicklay JJ / Xing L / Warren C / Anson B / Wang WL / Burgos ES / Ruff SE / Shabanowitz J / Cheng RH / Hunt DF / Shechter D
CitationJournal: Cell Rep / Year: 2015
Title: Developmentally Regulated Post-translational Modification of Nucleoplasmin Controls Histone Sequestration and Deposition.
Authors: Takashi Onikubo / Joshua J Nicklay / Li Xing / Christopher Warren / Brandon Anson / Wei-Lin Wang / Emmanuel S Burgos / Sophie E Ruff / Jeffrey Shabanowitz / R Holland Cheng / Donald F Hunt / David Shechter /
Abstract: Nucleoplasmin (Npm) is an abundant histone chaperone in vertebrate oocytes and embryos. During embryogenesis, regulation of Npm histone binding is critical for its function in storing and releasing ...Nucleoplasmin (Npm) is an abundant histone chaperone in vertebrate oocytes and embryos. During embryogenesis, regulation of Npm histone binding is critical for its function in storing and releasing maternal histones to establish and maintain the zygotic epigenome. Here, we demonstrate that Xenopus laevis Npm post-translational modifications (PTMs) specific to the oocyte and egg promote either histone deposition or sequestration, respectively. Mass spectrometry and Npm phosphomimetic mutations used in chromatin assembly assays identified hyperphosphorylation on the N-terminal tail as a critical regulator for sequestration. C-terminal tail phosphorylation and PRMT5-catalyzed arginine methylation enhance nucleosome assembly by promoting histone interaction with the second acidic tract of Npm. Electron microscopy reconstructions of Npm and TTLL4 activity toward the C-terminal tail demonstrate that oocyte- and egg-specific PTMs cause Npm conformational changes. Our results reveal that PTMs regulate Npm chaperoning activity by modulating Npm conformation and Npm-histone interaction, leading to histone sequestration in the egg.
History
DepositionJan 27, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseApr 1, 2015-
UpdateApr 1, 2015-
Current statusApr 1, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.87
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.87
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_2866.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of egg nucleoplasmin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 120 pix.
= 150. Å		1.25 Å/pix.
x 120 pix.
= 150. Å		1.25 Å/pix.
x 120 pix.
= 150. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.87 / Movie #1: 1.87
Minimum - Maximum-4.59233284 - 7.07347488
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions120120120
Spacing120120120
CellA=B=C: 150.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z150.000150.000150.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS120120120
D min/max/mean-4.5927.0730.000

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Supplemental data

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Sample components

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Entire : reconstruction of egg Nucleoplasmin

EntireName: reconstruction of egg Nucleoplasmin
Components
  • Sample: reconstruction of egg Nucleoplasmin
  • Protein or peptide: nucleoplasmin

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Supramolecule #1000: reconstruction of egg Nucleoplasmin

SupramoleculeName: reconstruction of egg Nucleoplasmin / type: sample / ID: 1000 / Oligomeric state: pentamer / Number unique components: 1

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Macromolecule #1: nucleoplasmin

MacromoleculeName: nucleoplasmin / type: protein_or_peptide / ID: 1 / Oligomeric state: pentamer / Recombinant expression: No
Source (natural)Organism: Xenopus (frog) / Organelle: nucleus / Location in cell: nucleus

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: 2% uranyl acetate for 25 seconds
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2100F
DateMar 13, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 88 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 2400

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