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- PDB-7kbf: H1.8 bound nucleosome isolated from metaphase chromosome in Xenop... -

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Basic information

Entry
Database: PDB / ID: 7kbf
TitleH1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Components
  • (DNA (184-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Protein B4
KeywordsDNA BINDING PROTEIN / nucleosome / M phase / cell cycle / chromatin / Xenopus egg extract / H1 / Chromatosome / Linker histone
Function / homology
Function and homology information


DNA-templated transcription, initiation / nucleosome assembly / nucleosome / multicellular organism development / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
linker histone H1 and H5 family / Domain in histone families 1 and 5 / Linker histone H1/H5 globular (H15) domain profile. / Linker histone H1/H5, domain H15 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A ...linker histone H1 and H5 family / Domain in histone families 1 and 5 / Linker histone H1/H5 globular (H15) domain profile. / Linker histone H1/H5, domain H15 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / 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 H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA (> 100) / DNA (> 10) / DNA / Histone H2B 1.1 / Protein B4 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å
AuthorsArimura, Y. / Funabiki, H.
Funding support United States, Japan, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132111 United States
Japan Society for the Promotion of Science (JSPS)JSPS Overseas Research Fellowships Japan
CitationJournal: Mol Cell / Year: 2021
Title: Structural features of nucleosomes in interphase and metaphase chromosomes.
Authors: Yasuhiro Arimura / Rochelle M Shih / Ruby Froom / Hironori Funabiki /
Abstract: Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo- ...Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-22792
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (184-MER)
J: DNA (184-MER)
K: Protein B4


Theoretical massNumber of molelcules
Total (without water)246,91411
Polymers246,91411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55660 Å2
ΔGint-383 kcal/mol
Surface area88360 Å2

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.2 / Histone H3


Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P84233
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P62799
#3: Protein Histone H2A /


Mass: 14883.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6DKE3
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13965.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P02281
#7: Protein Protein B4 / Histone H1-like protein / Linker histone B4


Mass: 29387.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P15308

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (184-MER)


Mass: 53114.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#6: DNA chain DNA (184-MER)


Mass: 53083.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

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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: H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES-KOH1
230 mMKClKCl1
31 mMEGTAEGTA1
40.3 microg/mlLeupeptin1
50.3 microg/mlPepstatin1
60.3 microg/mlChymostatin1
71 mMSodium Butyrate1
81 mMbeta-glycerophosphate1
91 %trehalose1
100.1 %1,6,-hexanediol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector model
1138.34SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)
2135.27SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7PHENIXmodel fitting
9PHENIXmodel refinement
11cryoSPARC2.14final Euler assignment
12cryoSPARC2.14classification
13cryoSPARC2.143D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27383 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-ID
16DZT1
25NL01

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