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- PDB-2xql: Fitting of the H2A-H2B histones in the electron microscopy map of... -
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Basic information
Entry | Database: PDB / ID: 2xql | ||||||
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Title | Fitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5). | ||||||
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![]() | NUCLEAR PROTEIN / 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 | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 19.5 Å | ||||||
![]() | Ramos, I. / Martin-Benito, J. / Finn, R. / Bretana, L. / Aloria, K. / Arizmendi, J.M. / Ausio, J. / Muga, A. / Valpuesta, J.M. / 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. | ||||||
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PDBx/mmCIF format | ![]() | 175.5 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 791.1 KB | Display | ![]() |
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Full document | ![]() | 814.8 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
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-Related structure data
Related structure data | ![]() 1777MC ![]() 1778C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 10034.639 Da / Num. of mol.: 5 / Fragment: RESIDUES 16-106 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 9977.441 Da / Num. of mol.: 5 / Fragment: RESIDUES 37-126 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: NUCLEOPLASMIN H2A-H2B HISTONES COMPLEX. / Type: COMPLEX |
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Buffer solution | Name: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL / pH: 7.5 / Details: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Material: Uranyl Acetate |
Specimen support | Details: CARBON |
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Electron microscopy imaging
Microscopy | Model: JEOL 1200EXII |
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Electron gun | Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 5.6 mm |
Specimen holder | Temperature: 293 K |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 14 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: EACH PLATE | |||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | |||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 19.5 Å / Num. of particles: 5557 / Nominal pixel size: 2.3 Å Details: DOCKING OF FIVE DIMERS OF H2A-H2B HISTONES IN THE NUCLEOPLASMIN H2A-H2B COMPLEX (1 5-5). THE EXTENDED REGION OF THE H2A HISTONE WAS REMOVED. THE FINAL DOCKING INCLUDES THE FRAGMENTS FROM ...Details: DOCKING OF FIVE DIMERS OF H2A-H2B HISTONES IN THE NUCLEOPLASMIN H2A-H2B COMPLEX (1 5-5). THE EXTENDED REGION OF THE H2A HISTONE WAS REMOVED. THE FINAL DOCKING INCLUDES THE FRAGMENTS FROM AMINOACID 15 TO 105 OF H2A HISTONE AND 36 TO 125 OF H2B HISTONE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1777. (DEPOSITION ID: 7474). Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: METHOD--VOLUMETRIC CORRELATION REFINEMENT PROTOCOL--PROJECTION MATCHING | |||||||||||||||
Atomic model building | PDB-ID: 1AOI Accession code: 1AOI / Source name: PDB / Type: experimental model | |||||||||||||||
Refinement | Highest resolution: 19.5 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 19.5 Å
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