[English] 日本語
Yorodumi
- EMDB-40037: Composite map of the Hir complex with Asf1/H3/H4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40037
TitleComposite map of the Hir complex with Asf1/H3/H4
Map dataa composite map of the Hir with Asf1/H3/H4
Sample
  • Complex: the yeast Hir complex with Asf1/H3/H4
    • Complex: the yeast Hir complex
    • Complex: Asf1/H3/H4
KeywordsHistone / Complex / Replication-Independent / CHAPERONE
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) / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes ...negative regulation of chromatin organization / HIR complex / negative regulation of transcription by RNA polymerase III / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / nucleosome disassembly / SUMOylation of chromatin organization proteins / transcription elongation-coupled chromatin remodeling / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / chromosome, centromeric region / intracellular copper ion homeostasis / CENP-A containing nucleosome / aerobic respiration / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromosome / chromatin organization / histone binding / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
HIRA B motif / HIRA B motif / Hpc2-related domain / HPC2 and ubinuclein domain / Histone transcription regulator 3/CABIN1 / TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / : / CAF1B/HIR1 beta-propeller domain ...HIRA B motif / HIRA B motif / Hpc2-related domain / HPC2 and ubinuclein domain / Histone transcription regulator 3/CABIN1 / TUP1-like enhancer of split / WD repeat HIR1 / TUP1-like enhancer of split / : / CAF1B/HIR1 beta-propeller domain / 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 domain / Histone-fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone chaperone / Histone H4 / Protein HIR1 / Protein HIR2 / Histone transcription regulator 3 / Histone H3 / Histone promoter control protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsKim HJ / Murakami K
Funding support United States, 1 items
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 9, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40037.png

Downloads & links

-
Map

FileDownload / File: emd_40037.map.gz / Format: CCP4 / Size: 512.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationa composite map of the Hir with Asf1/H3/H4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 455 pix.
= 618.8 Å		1.36 Å/pix.
x 555 pix.
= 754.8 Å		1.36 Å/pix.
x 532 pix.
= 723.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum0.0 - 0.19019519
Average (Standard dev.)0.0059337444 (±0.0064093615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-126-117-63
Dimensions555532455
Spacing532555455
CellA: 723.52 Å / B: 754.8 Å / C: 618.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : the yeast Hir complex with Asf1/H3/H4

EntireName: the yeast Hir complex with Asf1/H3/H4
Components
  • Complex: the yeast Hir complex with Asf1/H3/H4
    • Complex: the yeast Hir complex
    • Complex: Asf1/H3/H4

-
Supramolecule #1: the yeast Hir complex with Asf1/H3/H4

SupramoleculeName: the yeast Hir complex with Asf1/H3/H4 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.24 MDa

-
Supramolecule #2: the yeast Hir complex

SupramoleculeName: the yeast Hir complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Supramolecule #3: Asf1/H3/H4

SupramoleculeName: Asf1/H3/H4 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 639000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more