+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-1777 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the complex Nucleoplamsin:H2A-H2B histones. | |||||||||
![]() | Electron microscopy map of the Nucleoplasmin-H2A-H2B histones complex (1-5-5) | |||||||||
![]() |
| |||||||||
![]() | Nucleoplasmin / histone H2A / histone H2B / chaperone / chromatin / nuclear-chaperone / histone-chaperone | |||||||||
Function / homology | ![]() Condensation of Prophase Chromosomes / Metalloprotease DUBs / UCH proteinases / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs ...Condensation of Prophase Chromosomes / Metalloprotease DUBs / UCH proteinases / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Ub-specific processing proteases / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.5 Å | |||||||||
![]() | Ramos I / Martin-Benito J / Finn R / Bretana L / Aloria K / Arizmendi JM / Ausio J / Muga A / Valpuesta JM / Prado A | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 1.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 12.5 KB 12.5 KB | Display Display | ![]() |
Images | ![]() | 757.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 201.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 201 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xqlMC ![]() 1778C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Electron microscopy map of the Nucleoplasmin-H2A-H2B histones complex (1-5-5) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).
Entire | Name: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5). |
---|---|
Components |
|
-Supramolecule #1000: Nucleoplasmin-Histone H2A-Histone H2B complex (1-5-5).
Supramolecule | Name: 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 weight | Experimental: 270 KDa / Theoretical: 270 KDa |
-Macromolecule #1: H2A Histone
Macromolecule | Name: 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: ![]() ![]() |
Molecular weight | Experimental: 13 KDa / Theoretical: 13 KDa |
Sequence | InterPro: Histone H2A |
-Macromolecule #2: H2B Histone
Macromolecule | Name: 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: ![]() ![]() |
Molecular weight | Experimental: 14 KDa / Theoretical: 14 KDa |
Sequence | InterPro: Histone H2B |
-Macromolecule #3: Nucleoplasmin
Macromolecule | Name: Nucleoplasmin / type: protein_or_peptide / ID: 3 / Name.synonym: Nucleoplasmin / Number of copies: 1 / Oligomeric state: Pentamer / Recombinant expression: No |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 110 KDa / Theoretical: 110 KDa |
Sequence | InterPro: Nucleoplasmin family |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 / Details: 2mM MgCl2, 240mM NaCl, 25 mM Tris-HCl |
---|---|
Staining | Type: NEGATIVE Details: Grids were stained with 2% w/v Uranyl Acetate solution for 1 minute. |
Grid | Details: 200 mesh CuRh Grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-
Electron microscopy
Microscope | JEOL 1200EXII |
---|---|
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Image recording | Category: 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 beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination 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 stage | Specimen holder: Eucentric / Specimen holder model: JEOL |
-
Image processing
CTF correction | Details: Each plate |
---|---|
Final reconstruction | Applied 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 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: C / Chain - #1 - Chain ID: D |
---|---|
Software | Name: SITUS |
Details | PDBEntryID_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. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-2xql: |