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- PDB-3c9k: Model of Histone Octamer Tubular Crystals -

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Basic information

Entry
Database: PDB / ID: 3c9k
TitleModel of Histone Octamer Tubular Crystals
Components
  • Histone H2A-IV
  • Histone H2B 7
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / helix / tubular crystal / Chromosomal protein / Nucleosome core / Nucleus / Phosphoprotein / Methylation
Function / homology
Function and homology information


PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Interleukin-7 signaling / Chromatin modifying enzymes ...PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Processing of DNA double-strand break ends / Interleukin-7 signaling / Chromatin modifying enzymes / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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 / Factors involved in megakaryocyte development and platelet production / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / protein-containing complex binding / DNA binding / nucleoplasm / 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 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A-IV / Histone H2B 7 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / cryo EM / Resolution: 20 Å
AuthorsFrouws, T.D.
CitationJournal: Biophys J / Year: 2009
Title: Histone octamer helical tubes suggest that an internucleosomal four-helix bundle stabilizes the chromatin fiber.
Authors: Timothy D Frouws / Hugh-G Patterton / Bryan T Sewell /
Abstract: A major question in chromatin involves the exact organization of nucleosomes within the 30-nm chromatin fiber and its structural determinants of assembly. Here we investigate the structure of histone ...A major question in chromatin involves the exact organization of nucleosomes within the 30-nm chromatin fiber and its structural determinants of assembly. Here we investigate the structure of histone octamer helical tubes via the method of iterative helical real-space reconstruction. Accurate placement of the x-ray structure of the histone octamer within the reconstructed density yields a pseudoatomic model for the entire helix, and allows precise identification of molecular interactions between neighboring octamers. One such interaction that would not be obscured by DNA in the nucleosome consists of a twofold symmetric four-helix bundle formed between pairs of H2B-alpha3 and H2B-alphaC helices of neighboring octamers. We believe that this interface can act as an internucleosomal four-helix bundle within the context of the chromatin fiber. The potential relevance of this interface in the folding of the 30-nm chromatin fiber is discussed.
History
DepositionFeb 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Data collection / Database references
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as representative helical assembly
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Assembly

Deposited unit
A: Histone H2A-IV
B: Histone H2B 7
C: Histone H3.2
D: Histone H4
E: Histone H2A-IV
F: Histone H2B 7
G: Histone H3.2
H: Histone H4


Theoretical massNumber of molelcules
Total (without water)108,5118
Polymers108,5118
Non-polymers00
Water00
1
A: Histone H2A-IV
B: Histone H2B 7
C: Histone H3.2
D: Histone H4
E: Histone H2A-IV
F: Histone H2B 7
G: Histone H3.2
H: Histone H4
x 88


Theoretical massNumber of molelcules
Total (without water)9,548,950704
Polymers9,548,950704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation87
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 11 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 88 / Rise per n subunits: 65.12 Å / Rotation per n subunits: -7.56 °)

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Components

#1: Protein Histone H2A-IV


Mass: 13838.167 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Blood, Erythrocytes / References: UniProt: P02263
#2: Protein Histone H2B 7 / H2B VII


Mass: 13864.097 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Blood, Erythrocytes / References: UniProt: P0C1H5
#3: Protein Histone H3.2


Mass: 15289.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Blood, Erythrocytes / References: UniProt: P84229
#4: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Blood, Erythrocytes / References: UniProt: P62801

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Histone Octamer Tubular Crystal / Type: COMPLEX
Details: Histone Octamers are assembled into ring with 11-fold rotational symmetry, rings are further stacked via helical symmetry
Buffer solutionName: 100mM Tris-HCl, 2M NaCl, 40% NH2SO4 / pH: 7.4 / Details: 100mM Tris-HCl, 2M NaCl, 40% NH2SO4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: 300 mesh continous carbon grids
VitrificationDetails: Negative Stain 0.2% Uranyl Acetate

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Electron microscopy imaging

MicroscopyModel: ZEISS LEO912
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 800 nm / Nominal defocus min: 1000 nm
Specimen holderTemperature: 295 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 100 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
3D reconstructionMethod: Iterative Helical Real Space Reconstruction / Resolution: 20 Å / Num. of particles: 3500 / Nominal pixel size: 4 Å / Actual pixel size: 4 Å
Details: 11-fold rotational symmetry imposed during backprojection
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation and van der Waals energy
Details: METHOD--Because of the helical line group, the dyad axis is constrained to lie facing the helical axis and reduces the search to rotations and translations about this dyad REFINEMENT ...Details: METHOD--Because of the helical line group, the dyad axis is constrained to lie facing the helical axis and reduces the search to rotations and translations about this dyad REFINEMENT PROTOCOL--Constrained Rigid Body
Atomic model buildingPDB-ID: 2HIO

2hio


Accession code: 2HIO / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 0 0 5700

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