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- EMDB-1777: Structure of the complex Nucleoplamsin:H2A-H2B histones. -

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Basic information

Entry
Database: EMDB / ID: EMD-1777
TitleStructure of the complex Nucleoplamsin:H2A-H2B histones.
Map dataElectron microscopy map of the Nucleoplasmin-H2A-H2B histones complex (1-5-5)
Sample
  • Sample: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).
  • Protein or peptide: H2A Histone
  • Protein or peptide: H2B Histone
  • Protein or peptide: Nucleoplasmin
KeywordsNucleoplasmin / histone H2A / histone H2B / chaperone / chromatin / nuclear-chaperone / histone-chaperone
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Metalloprotease DUBs / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones ...Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Metalloprotease DUBs / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / UCH proteinases / B-WICH complex positively regulates rRNA expression / Ub-specific processing proteases / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Nucleoplasmin family / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Nucleoplasmin family / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A-IV / Histone H2B 5
Similarity search - Component
Biological speciesGallus gallus (chicken) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / negative staining / Resolution: 19.5 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: 3.65
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.65
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xql
  • Surface level: 3.65
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xql
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1777.tif

Downloads & links

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Map

FileDownload / File: emd_1777.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron microscopy map of the Nucleoplasmin-H2A-H2B histones complex (1-5-5)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 100 pix.
= 230. Å		2.3 Å/pix.
x 100 pix.
= 230. Å		2.3 Å/pix.
x 100 pix.
= 230. 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: 3.65 / Movie #1: 3.65
Minimum - Maximum-3.24812 - 9.92155
Average (Standard dev.)-0.00000000702345 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 230 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z230.000230.000230.000
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/NS100100100
D min/max/mean-3.2489.922-0.000

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Supplemental data

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Sample components

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Entire : Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).

EntireName: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).
Components
  • Sample: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).
  • Protein or peptide: H2A Histone
  • Protein or peptide: H2B Histone
  • Protein or peptide: Nucleoplasmin

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Supramolecule #1000: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).

SupramoleculeName: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).
type: sample / ID: 1000
Oligomeric state: One Molecule of Nucleoplasmin binds to five dimers of H2A-H2B histones
Number unique components: 3
Molecular weightExperimental: 270 KDa / Theoretical: 270 KDa

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Macromolecule #1: H2A Histone

MacromoleculeName: H2A Histone / type: protein_or_peptide / ID: 1 / Name.synonym: H2A Histone / Number of copies: 5 / Oligomeric state: Forming a Heterodimer with H2B / Recombinant expression: No
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Cell: Erythrocyte
Molecular weightExperimental: 13 KDa / Theoretical: 13 KDa
SequenceInterPro: Histone H2A

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Macromolecule #2: H2B Histone

MacromoleculeName: H2B Histone / type: protein_or_peptide / ID: 2 / Name.synonym: H2B Histone / Number of copies: 5 / Oligomeric state: Forming a Heterodimer with H2A / Recombinant expression: No
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Cell: Erythrocyte
Molecular weightExperimental: 14 KDa / Theoretical: 14 KDa
SequenceInterPro: Histone H2B

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Macromolecule #3: Nucleoplasmin

MacromoleculeName: Nucleoplasmin / type: protein_or_peptide / ID: 3 / Name.synonym: Nucleoplasmin / Number of copies: 1 / Oligomeric state: Pentamer / Recombinant expression: No
Source (natural)Organism: Xenopus laevis (African clawed frog) / synonym: African clawed frog / Tissue: Egg / Cell: Oocyte / Organelle: Nucleus / Location in cell: 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: 14 / 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: 19.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, XMIPP, SPIDER / Number images used: 5557

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Atomic model buiding 1

Initial modelPDB ID:

1aoi


Chain - #0 - Chain ID: C / Chain - #1 - Chain ID: D
SoftwareName: SITUS
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. A dimer of H2A-H2B histones was fitted in Map and refined using COLORES software (SITUS package). Afterwards, the 5 fold symmetry was applied to the fitted structure.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2xql:
Fitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).

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