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- EMDB-1778: Structure of the Nuclear Chaperone Nucleoplamsin. -

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Basic information

Entry
Database: EMDB / ID: EMD-1778
TitleStructure of the Nuclear Chaperone Nucleoplamsin.
Map dataThis a map of the nuclear chaperone nucleoplasmin.
Sample
  • Sample: Nucleoplasmin chaperone
  • Protein or peptide: Nucleoplasmin
KeywordsNucleoplasmin / Histone H2A / Histone H2B / Chaperone / Chromatin / Nuclear-chaperone / Histone-chaperone
Function / homologyNucleoplasmin family
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsRamos I / Martin-Benito J / Finn R / Bretana L / Aloria K / Arizmendi JM / Ausio J / Muga A / Valpuesta JM / Prado A
CitationJournal: J Biol Chem / Year: 2010
Title: Nucleoplasmin binds histone H2A-H2B dimers through its distal face.
Authors: Isbaal Ramos / Jaime Martín-Benito / Ron Finn / Laura Bretaña / Kerman Aloria / Jesús M Arizmendi / Juan Ausió / Arturo Muga / José M Valpuesta / Adelina Prado /
Abstract: Nucleoplasmin (NP) is a pentameric chaperone that regulates the condensation state of chromatin extracting specific basic proteins from sperm chromatin and depositing H2A-H2B histone dimers. It has ...Nucleoplasmin (NP) is a pentameric chaperone that regulates the condensation state of chromatin extracting specific basic proteins from sperm chromatin and depositing H2A-H2B histone dimers. It has been proposed that histones could bind to either the lateral or distal face of the pentameric structure. Here, we combine different biochemical and biophysical techniques to show that natural, hyperphosphorylated NP can bind five H2A-H2B dimers and that the amount of bound ligand depends on the overall charge (phosphorylation level) of the chaperone. Three-dimensional reconstruction of NP/H2A-H2B complex carried out by electron microscopy reveals that histones interact with the chaperone distal face. Limited proteolysis and mass spectrometry indicate that the interaction results in protection of the histone fold and most of the H2A and H2B C-terminal tails. This structural information can help to understand the function of NP as a histone chaperone.
History
DepositionAug 31, 2010-
Header (metadata) releaseOct 26, 2010-
Map releaseOct 26, 2010-
UpdateOct 26, 2010-
Current statusOct 26, 2010Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1778.tif

Downloads & links

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Map

FileDownload / File: emd_1778.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis a map of the nuclear chaperone nucleoplasmin.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 80 pix.
= 184. Å		2.3 Å/pix.
x 80 pix.
= 184. Å		2.3 Å/pix.
x 80 pix.
= 184. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0225 / Movie #1: 0.0225
Minimum - Maximum-0.0623846 - 0.089064
Average (Standard dev.)-0.000197456 (±0.00908658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 184 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z184.000184.000184.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.0620.089-0.000

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Supplemental data

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Sample components

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Entire : Nucleoplasmin chaperone

EntireName: Nucleoplasmin chaperone
Components
  • Sample: Nucleoplasmin chaperone
  • Protein or peptide: Nucleoplasmin

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Supramolecule #1000: Nucleoplasmin chaperone

SupramoleculeName: Nucleoplasmin chaperone / type: sample / ID: 1000 / Oligomeric state: Pentameric / Number unique components: 1
Molecular weightExperimental: 110 KDa / Theoretical: 110 KDa

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Macromolecule #1: Nucleoplasmin

MacromoleculeName: Nucleoplasmin / type: protein_or_peptide / ID: 1 / Name.synonym: Nucleoplasmin / Number of copies: 5 / Oligomeric state: Pentamer / Recombinant expression: No
Source (natural)Organism: Xenopus laevis (African clawed frog) / synonym: African clawed frog / Tissue: Egg / Cell: Oocyte / Organelle: Nucleus
Molecular weightExperimental: 110 KDa / Theoretical: 110 KDa
SequenceInterPro: Nucleoplasmin family

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 2mM MgCl2, 240mM NaCl, 25 mM Tris-HCl
StainingType: NEGATIVE
Details: Grids were stained with 2% w/v Uranyl Acetate solution for 1 minute.
GridDetails: 200 mesh CuRh grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1200EXII
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 2.3 µm / Number real images: 10 / Details: downsampling factor of 2 / Bits/pixel: 8
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: Each plate
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, XMIPP, SPIDER / Number images used: 9862

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