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- EMDB-1469: Iterative Helical Real Space Reconstruction of Histone Octamer He... -

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Basic information

Entry
Database: EMDB / ID: EMD-1469
TitleIterative Helical Real Space Reconstruction of Histone Octamer Helical Tubes
Map datasurface rendering of histone octamer tubular crystal
Sample
  • Sample: Histone Octamer Tubular Crystals
  • Protein or peptide: histone H2A
  • Protein or peptide: histone H2B
  • Protein or peptide: histone H3
  • Protein or peptide: histone H4
Keywordshistone / octamer / H2A / H2B / H3 / H4 / nucleosome / IHRSR / helical / tubular crystal
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 / Metalloprotease DUBs / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...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 / Metalloprotease DUBs / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Interleukin-7 signaling / Chromatin modifying enzymes / HATs acetylate histones / Ub-specific processing proteases / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / 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 / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / structural constituent of chromatin / nucleosome / protein heterodimerization activity / protein-containing complex binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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)
Methodhelical reconstruction / negative staining / Resolution: 20.0 Å
AuthorsFrouws TD / Patterton HG / Sewell BT
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 13, 2008-
Header (metadata) releaseFeb 13, 2008-
Map releaseApr 20, 2009-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1469.gif

Downloads & links

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Map

FileDownload / File: emd_1469.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsurface rendering of histone octamer tubular crystal
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 128 pix.
= 512. Å		4 Å/pix.
x 128 pix.
= 512. Å		4 Å/pix.
x 128 pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.0260648 - 0.04370119
Average (Standard dev.)0.00259267 (±0.00934648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 512.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0260.0440.003

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Supplemental data

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Sample components

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Entire : Histone Octamer Tubular Crystals

EntireName: Histone Octamer Tubular Crystals
Components
  • Sample: Histone Octamer Tubular Crystals
  • Protein or peptide: histone H2A
  • Protein or peptide: histone H2B
  • Protein or peptide: histone H3
  • Protein or peptide: histone H4

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Supramolecule #1000: Histone Octamer Tubular Crystals

SupramoleculeName: Histone Octamer Tubular Crystals / type: sample / ID: 1000 / Details: crystalline tubes / Oligomeric state: octameric, C11, and helical / Number unique components: 4
Molecular weightExperimental: 109 KDa / Theoretical: 109 KDa / Method: sequence

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Macromolecule #1: histone H2A

MacromoleculeName: histone H2A / type: protein_or_peptide / ID: 1 / Name.synonym: H2A / Details: Histone octamers purified from chicken blood / Number of copies: 2 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: Blood / Cell: Erythrocytes / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 14 KDa / Theoretical: 14 KDa
SequenceInterPro: Histone H2A

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Macromolecule #2: histone H2B

MacromoleculeName: histone H2B / type: protein_or_peptide / ID: 2 / Name.synonym: H2B / Details: Histone octamers purified from chicken blood / Number of copies: 2 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: Blood / Cell: Erythrocytes / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 14 KDa / Theoretical: 14 KDa
SequenceInterPro: Histone H2B

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Macromolecule #3: histone H3

MacromoleculeName: histone H3 / type: protein_or_peptide / ID: 3 / Name.synonym: H3 / Details: Histone octamers purified from chicken blood / Number of copies: 2 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: Blood / Cell: Erythrocytes / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 15 KDa / Theoretical: 15 KDa
SequenceInterPro: Histone H3/CENP-A

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Macromolecule #4: histone H4

MacromoleculeName: histone H4 / type: protein_or_peptide / ID: 4 / Name.synonym: H4 / Details: Histone octamers purified from chicken blood / Number of copies: 2 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Tissue: Blood / Cell: Erythrocytes / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 11 KDa / Theoretical: 11 KDa
SequenceInterPro: Histone H4

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4 / Details: 100mM Tris-HCl, 2M NaCl, 40% NH2SO4
StainingType: NEGATIVE
Details: 5 ul 0.4% Uranyl Acetate is added to 5 ul sample, grid is floated on mixture for 1 min, then washed twice with 10 ul 0.2% Uranyl Acetate drops.
GridDetails: 300 Mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER
Detailsdouble dialysis

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Electron microscopy

MicroscopeZEISS LEO912
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: Omega in-column / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
TemperatureAverage: 295 K
Alignment procedureLegacy - Astigmatism: corrected at 80,000 times magnification
DetailsZeiss LEO 912 microscope using low dose technique
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 2 µm / Number real images: 50 / Average electron dose: 100 e/Å2
Details: scanned on Ilford Leafscan at 2A per pixel and binned to 4A per pixel
Od range: 1 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

Final angle assignmentDetails: Single axis tilt geometry. 4.1 degree increment for phi to cover an asymmetric wedge of 32.72 degrees. Therefore 8 reference projections.
Final reconstructionApplied symmetry - Helical parameters - Δz: 65.12 Å
Applied symmetry - Helical parameters - Δ&Phi: 7.56 °
Applied symmetry - Helical parameters - Axial symmetry: D11 (2x11 fold dihedral)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: helical symmetry is searched for and imposed each iteration round on the backprojected volume.
DetailsHelices segmented into overlapping boxes using Boxer program from EMAN

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Atomic model buiding 1

Initial modelPDB ID:

2hio

SoftwareName: SPIDER
DetailsProtocol: Rigid body. Because of helical line group, the dyad axis is constrained to lie facing the helical axis and reduces the search to 2D. i.e. to rotations and translations about this dyad.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC and VdW
Output model

PDB-3c9k:
Model of Histone Octamer Tubular Crystals

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