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- PDB-2xql: Fitting of the H2A-H2B histones in the electron microscopy map of... -

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Database: PDB / ID: 2xql
TitleFitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).
Components
  • HISTONE H2A-IV
  • HISTONE H2B 5
KeywordsNUCLEAR PROTEIN / 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
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 19.5 Å
AuthorsRamos, I. / Martin-Benito, J. / Finn, R. / Bretana, L. / Aloria, K. / Arizmendi, J.M. / Ausio, J. / Muga, A. / Valpuesta, J.M. / 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
DepositionSep 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Derived calculations / Other / Version format compliance
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Simplified surface model + fitted atomic model
  • EMDB-1777
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Structure viewerMolecule:
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Assembly

Deposited unit
A: HISTONE H2A-IV
B: HISTONE H2B 5
C: HISTONE H2A-IV
D: HISTONE H2B 5
E: HISTONE H2A-IV
F: HISTONE H2B 5
G: HISTONE H2A-IV
H: HISTONE H2B 5
I: HISTONE H2A-IV
J: HISTONE H2B 5


Theoretical massNumber of molelcules
Total (without water)100,06010
Polymers100,06010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
HISTONE H2A-IV / H2A HISTONE


Mass: 10034.639 Da / Num. of mol.: 5 / Fragment: RESIDUES 16-106 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Cell: ERYTHROCYTE / References: UniProt: P02263
#2: Protein
HISTONE H2B 5 / H2B HISTONE / H2B V


Mass: 9977.441 Da / Num. of mol.: 5 / Fragment: RESIDUES 37-126 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Cell: ERYTHROCYTE / References: UniProt: P0C1H4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NUCLEOPLASMIN H2A-H2B HISTONES COMPLEX. / Type: COMPLEX
Buffer solutionName: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL / pH: 7.5 / Details: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyModel: JEOL 1200EXII
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 5.6 mm
Specimen holderTemperature: 293 K
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 14
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2EMAN3D reconstruction
3SPIDER3D reconstruction
4Xmipp3D reconstruction
CTF correctionDetails: EACH PLATE
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionMethod: 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 buildingProtocol: OTHER / Space: REAL
Details: METHOD--VOLUMETRIC CORRELATION REFINEMENT PROTOCOL--PROJECTION MATCHING
Atomic model buildingPDB-ID: 1AOI

1aoi


Accession code: 1AOI / Source name: PDB / Type: experimental model
RefinementHighest resolution: 19.5 Å
Refinement stepCycle: LAST / Highest resolution: 19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7030 0 0 0 7030

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