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- EMDB-30591: Cryo-EM structure of the nucleosome containing Giardia histones -

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Basic information

Entry
Database: EMDB / ID: EMD-30591
TitleCryo-EM structure of the nucleosome containing Giardia histones
Map dataNucleosome containing G. lamblia histones
Sample
  • Complex: Nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H2A
    • DNA: 601L DNA (145-MER)
    • DNA: 601L DNA (145-MER)
Function / homology
Function and homology information


nucleosome / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone H2B / Histone H2B / Histone H2A / Histone 2A / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 / Histone H3/CENP-A ...Histone H2B / Histone H2B / Histone H2A / Histone 2A / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A / Histone H4 / Histone H3 / Histone H2B
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsSato S / Takizawa Y / Kurumizaka H
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K06609 Japan
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones.
Authors: Shoko Sato / Yoshimasa Takizawa / Fumika Hoshikawa / Mariko Dacher / Hiroki Tanaka / Hiroaki Tachiwana / Tomoya Kujirai / Yukari Iikura / Cheng-Han Ho / Naruhiko Adachi / Indu Patwal / ...Authors: Shoko Sato / Yoshimasa Takizawa / Fumika Hoshikawa / Mariko Dacher / Hiroki Tanaka / Hiroaki Tachiwana / Tomoya Kujirai / Yukari Iikura / Cheng-Han Ho / Naruhiko Adachi / Indu Patwal / Andrew Flaus / Hitoshi Kurumizaka /
Abstract: Giardia lamblia is a pathogenic unicellular eukaryotic parasite that causes giardiasis. Its genome encodes the canonical histones H2A, H2B, H3, and H4, which share low amino acid sequence identity ...Giardia lamblia is a pathogenic unicellular eukaryotic parasite that causes giardiasis. Its genome encodes the canonical histones H2A, H2B, H3, and H4, which share low amino acid sequence identity with their human orthologues. We determined the structure of the G. lamblia nucleosome core particle (NCP) at 3.6 Å resolution by cryo-electron microscopy. G. lamblia histones form a characteristic NCP, in which the visible 125 base-pair region of the DNA is wrapped in a left-handed supercoil. The acidic patch on the G. lamblia octamer is deeper, due to an insertion extending the H2B α1 helix and L1 loop, and thus cannot bind the LANA acidic patch binding peptide. The DNA and histone regions near the DNA entry-exit sites could not be assigned, suggesting that these regions are asymmetrically flexible in the G. lamblia NCP. Characterization by thermal unfolding in solution revealed that both the H2A-H2B and DNA association with the G. lamblia H3-H4 were weaker than those for human H3-H4. These results demonstrate the uniformity of the histone octamer as the organizing platform for eukaryotic chromatin, but also illustrate the unrecognized capability for large scale sequence variations that enable the adaptability of histone octamer surfaces and confer internal stability.
History
DepositionSep 29, 2020-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d69
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30591.png

Downloads & links

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Map

FileDownload / File: emd_30591.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNucleosome containing G. lamblia histones
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 3.2 / Movie #1: 3.2
Minimum - Maximum-15.833427 - 25.902576
Average (Standard dev.)4.0890716e-10 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000168.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-113-15
NX/NY/NZ10616274
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-15.83325.9030.000

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Supplemental data

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Sample components

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Entire : Nucleosome

EntireName: Nucleosome
Components
  • Complex: Nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H2A
    • DNA: 601L DNA (145-MER)
    • DNA: 601L DNA (145-MER)

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Supramolecule #1: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Giardia intestinalis (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis (eukaryote)
Molecular weightTheoretical: 16.639574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKHT ARKTTSATKA PRKTIARKAA RKTASSTSGI KKTGRKKQGM VAVKEIKKYQ KSTDLLIRKL PFSKLVRDIV TSGLSKSDI RFQGAAVEAL QESAENYIIS LFVDTQLCAE HAKRVTIMKP DMELATRIGK RIEPEYRKGK

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis (eukaryote)
Molecular weightTheoretical: 11.407195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGKGKG KGYGKSKRHS KEKDTLGGIT KPAIRRLARR GGVKRISSTI YQQTREVLKA FLEVVLRDSL TYTEHGQRKT VTSQDVVYA LKRQGRTLYG FGI

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Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis (eukaryote)
Molecular weightTheoretical: 14.903089 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSKVETK RLMKKTEAGD KGDAKRKHKR HETYATYIYK VLRSENIRSE ADTDLGISNK GMEVMNSLVN DLFERIASEA SNLAKISKR NTIGKKDIES AAKLVIPGEI GRLIRDEADK ALSKFTSSKE STKK

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Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Giardia intestinalis (eukaryote)
Molecular weightTheoretical: 14.188249 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSTKPVK DNSKMKSRSA RAGISFPIGR IHRHLREGRY AERISSDAPV YLAAVLENVV AEVFREACNH RDKKSQKRIV PNHILTALR KDKELATIFA NVTIREGGVA RSAKEGREGK GSHRSQDL

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Macromolecule #5: 601L DNA (145-MER)

MacromoleculeName: 601L DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.761523 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DG)(DA)(DA)(DT)(DC)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DG)(DT)(DG) (DA)(DT)

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Macromolecule #6: 601L DNA (145-MER)

MacromoleculeName: 601L DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.752508 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DG)(DA)(DT)(DT)(DC)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DG)(DT)(DG) (DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194041
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7d69:
Cryo-EM structure of the nucleosome containing Giardia histones

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