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- PDB-8ghm: Hir1 WD40 domains and Asf1/H3/H4 -

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Basic information

Entry
Database: PDB / ID: 8ghm
TitleHir1 WD40 domains and Asf1/H3/H4
Components
  • Histone H3
  • Histone H4
  • Histone chaperone
  • Histone promoter control protein 2
  • Histone transcription regulator 3
  • Protein HIR1
KeywordsCHAPERONE / Histone / Complex / Replication-Independent
Function / homology
Function and homology information


negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA replication-dependent chromatin assembly / nucleosome disassembly / rRNA transcription / chromosome, centromeric region / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA replication-dependent chromatin assembly / nucleosome disassembly / rRNA transcription / chromosome, centromeric region / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / nucleosome assembly / transcription corepressor activity / structural constituent of chromatin / nucleosome / chromatin organization / chromosome / histone binding / chromatin remodeling / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
Hpc2-related domain / HIRA B motif / HPC2 and ubinuclein domain / HIRA B motif / TUP1-like enhancer of split / WD repeat HIR1 / Histone transcription regulator 3/CABIN1 / TUP1-like enhancer of split / Histone deposition protein Asf1 / Histone chaperone ASF1-like ...Hpc2-related domain / HIRA B motif / HPC2 and ubinuclein domain / HIRA B motif / TUP1-like enhancer of split / WD repeat HIR1 / Histone transcription regulator 3/CABIN1 / TUP1-like enhancer of split / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H4 / Histone H3 / Histone chaperone / Protein HIR1 / Histone transcription regulator 3 / Histone promoter control protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsKim, H.J. / Murakami, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123233 United States
CitationJournal: Mol Cell / Year: 2024
Title: Structure of the Hir histone chaperone complex.
Authors: Hee Jong Kim / Mary R Szurgot / Trevor van Eeuwen / M Daniel Ricketts / Pratik Basnet / Athena L Zhang / Austin Vogt / Samah Sharmin / Craig D Kaplan / Benjamin A Garcia / Ronen Marmorstein / Kenji Murakami /
Abstract: The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4) tetramers on DNA for replication-independent chromatin assembly. The ...The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4) tetramers on DNA for replication-independent chromatin assembly. The molecular architecture of the HIRA/Hir complex and its mode of histone deposition have remained unknown. Here, we report the cryo-EM structure of the S. cerevisiae Hir complex with Asf1/H3/H4 at 2.9-6.8 Å resolution. We find that the Hir complex forms an arc-shaped dimer with a Hir1/Hir2/Hir3/Hpc2 stoichiometry of 2/4/2/4. The core of the complex containing two Hir1/Hir2/Hir2 trimers and N-terminal segments of Hir3 forms a central cavity containing two copies of Hpc2, with one engaged by Asf1/H3/H4, in a suitable position to accommodate a histone (H3/H4) tetramer, while the C-terminal segments of Hir3 harbor nucleic acid binding activity to wrap DNA around the Hpc2-assisted histone tetramer. The structure suggests a model for how the Hir/Asf1 complex promotes the formation of histone tetramers for their subsequent deposition onto DNA.
History
DepositionMar 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein HIR1
M: Histone H3
N: Histone H4
O: Histone chaperone
J: Histone transcription regulator 3
D: Histone transcription regulator 3
G: Protein HIR1
F: Histone promoter control protein 2
L: Histone promoter control protein 2


Theoretical massNumber of molelcules
Total (without water)765,9689
Polymers765,9689
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 9 molecules AGMNOJDFL

#1: Protein Protein HIR1 / Histone transcription regulator 1


Mass: 93983.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32479
#2: Protein Histone H3


Mass: 15391.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HHT2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q536
#3: Protein Histone H4


Mass: 11395.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HHF1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q1V3
#4: Protein Histone chaperone / Asf1


Mass: 31629.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ASF1, GI527_G0003133 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L0YDQ7
#5: Protein Histone transcription regulator 3


Mass: 191915.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47171
#6: Protein Histone promoter control protein 2


Mass: 67877.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01448

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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

Component
IDNameTypeEntity IDParent-IDSource
1Hir1 WD40 domains and Asf1/H3/H4COMPLEXall0MULTIPLE SOURCES
2Hir1 WD40 bound Hpc2COMPLEX#1, #5-#61NATURAL
3Asf1/H3/H4COMPLEX#2-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
43Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.6
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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 366702 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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