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

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Basic information

Entry
Database: PDB / ID: 7d69
TitleCryo-EM structure of the nucleosome containing Giardia histones
Components
  • (601L DNA (145- ...) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
KeywordsNUCLEAR PROTEIN / nucleosome / chromatin / histone / Giardia lamblia
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
DNA / DNA (> 10) / DNA (> 100) / Histone H2A / Histone H4 / Histone H3 / Histone H2B
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsSato, S. / Takizawa, Y. / Kurumizaka, H.
Funding support Japan, 1items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-30591
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Histone H3
B: Histone H4
D: Histone H2B
E: Histone H3
F: Histone H4
H: Histone H2B
C: Histone H2A
G: Histone H2A
I: 601L DNA (145-MER)
J: 601L DNA (145-MER)


Theoretical massNumber of molelcules
Total (without water)203,79010
Polymers203,79010
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area50510 Å2
ΔGint-340 kcal/mol
Surface area61390 Å2

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Components

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Protein , 4 types, 8 molecules AEBFDHCG

#1: Protein Histone H3 /


Mass: 16639.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Gene: DHA2_154455 / Production host: Escherichia coli (E. coli) / References: UniProt: V6TEE9
#2: Protein Histone H4 /


Mass: 11407.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Gene: DHA2_135001, DHA2_154716, GSB_155602 / Production host: Escherichia coli (E. coli) / References: UniProt: E2RU60
#3: Protein Histone H2B /


Mass: 14903.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Gene: DHA2_151009 / Production host: Escherichia coli (E. coli) / References: UniProt: V6TJV6
#4: Protein Histone H2A /


Mass: 14188.249 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: E2RU15

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601L DNA (145- ... , 2 types, 2 molecules IJ

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


Mass: 44761.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain 601L DNA (145-MER)


Mass: 44752.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: Nucleosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Giardia intestinalis (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194041 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00911542
ELECTRON MICROSCOPYf_angle_d0.87416637
ELECTRON MICROSCOPYf_dihedral_angle_d25.5666116
ELECTRON MICROSCOPYf_chiral_restr0.0541902
ELECTRON MICROSCOPYf_plane_restr0.0051240

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