[English] 日本語
Yorodumi
- EMDB-45981: Medusavirus Nucleosome Core Particle Native -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45981
TitleMedusavirus Nucleosome Core Particle Native
Map dataMedusavirus medusae Nucleosome-like particle Native
Sample
  • Complex: Medusavirus Nucleosome Core Particle
    • Complex: Histone Complex
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: WIDOM 601 DNA
      • DNA: WIDOM 601 DNA (207 MER) strand 1
      • DNA: WIDOM 601 DNA (207 MER) Strand 2
KeywordsDNA Protein Complex / Nucleosome / Giant Virus / NCLDV / DNA BINDING PROTEIN
Biological speciesMedusavirus / synthetic construct (others) / Medusavirus medusae
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsToner CM / Luger K
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2024
Title: Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone.
Authors: Chelsea M Toner / Nicole M Hoitsma / Sashi Weerawarana / Karolin Luger /
Abstract: The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the ...The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the Nucleocytoplasmic Large DNA Viruses (NCLDV) encode histone-like proteins that in Melbournevirus were shown to form nucleosome-like particles. Medusavirus medusae (MM), a distantly related giant virus, encodes all four core histone proteins and, unique amongst most giant viruses, a putative acidic protein with two domains resembling eukaryotic linker histone H1. Here, we report the structure of nucleosomes assembled with MM histones and highlight similarities and differences with eukaryotic and Melbournevirus nucleosomes. Our structure provides insight into how variations in histone tail and loop lengths are accommodated within the context of the nucleosome. We show that MM-histones assemble into tri-nucleosome arrays, and that the putative linker histone H1 does not function in chromatin compaction. These findings expand our limited understanding of chromatin organization by virus-encoded histones.
History
DepositionJul 30, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45981.png

Downloads & links

-
Map

FileDownload / File: emd_45981.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMedusavirus medusae Nucleosome-like particle Native
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 256 pix.
= 260.352 Å		1.02 Å/pix.
x 256 pix.
= 260.352 Å		1.02 Å/pix.
x 256 pix.
= 260.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.017 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.118
Minimum - Maximum-0.23283798 - 0.51211643
Average (Standard dev.)0.0014235482 (±0.0198117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 260.352 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Medusavirus medusae Nucleosome-like particle Native half map A

Fileemd_45981_half_map_1.map
AnnotationMedusavirus medusae Nucleosome-like particle Native half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Medusavirus medusae Nucleosome-like particle Native half map B

Fileemd_45981_half_map_2.map
AnnotationMedusavirus medusae Nucleosome-like particle Native half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Medusavirus Nucleosome Core Particle

EntireName: Medusavirus Nucleosome Core Particle
Components
  • Complex: Medusavirus Nucleosome Core Particle
    • Complex: Histone Complex
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: WIDOM 601 DNA
      • DNA: WIDOM 601 DNA (207 MER) strand 1
      • DNA: WIDOM 601 DNA (207 MER) Strand 2

-
Supramolecule #1: Medusavirus Nucleosome Core Particle

SupramoleculeName: Medusavirus Nucleosome Core Particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Histone Complex

SupramoleculeName: Histone Complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Medusavirus

-
Supramolecule #3: WIDOM 601 DNA

SupramoleculeName: WIDOM 601 DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus medusae
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMPKERAI KKSKSAVKKV AEKKAAIKSK AKKAATGVKK PHRFRPGTTA KRLSKKEQKL SSTKTTVRRA PFGRIVRTIA SLSSADSMRF SANAVDLLQQ GIELYMLDLM KNAALAAKQA KRMTLMGKDI DLIQTANHEM ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMPKERAI KKSKSAVKKV AEKKAAIKSK AKKAATGVKK PHRFRPGTTA KRLSKKEQKL SSTKTTVRRA PFGRIVRTIA SLSSADSMRF SANAVDLLQQ GIELYMLDLM KNAALAAKQA KRMTLMGKDI DLIQTANHEM IDEAHAAKLA NTSSAGFARR RVTKKE

-
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus medusae
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMPKKIAA RRSSKHIKNL GEEIGNSAVR KTVLRTGVVF RLDKTVRPKF HKVMLSKLYE AVNIAKLAAK HSGRSTIQPK DVRLGLKLAS IKLLA

-
Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus medusae
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMEIDSHV QPAEVLAAAS ESMQLEEQTQ LPASAAGEAL EELQTEGKKT SPAKKRTSSG KNVKRANERA GLKLPPGRIQ KIIKANQTTD VGRSSPTASV FLTAVIEDIV KEIIKGADKK SEERGRIRIS PQDILKYLTE ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMEIDSHV QPAEVLAAAS ESMQLEEQTQ LPASAAGEAL EELQTEGKKT SPAKKRTSSG KNVKRANERA GLKLPPGRIQ KIIKANQTTD VGRSSPTASV FLTAVIEDIV KEIIKGADKK SEERGRIRIS PQDILKYLTE NGEAYMHILG DAFVSHGGVG QVAEMAAAAA NTGIKKRKRA ASTAEGAPKK KIAKKAAAKK ATGAKKVVKK KSGSTKSKTT GKSVTKKASS RKVASA

-
Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Medusavirus medusae
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMSQIDEH VTEMTEFEAE HESTYSEHSD EEEQELGARV PSRKQKGKAA AKKVKKAVAK KSGEERRRKK NYDSFATFIA KLVGPNGKGR KPGFSAKGME VLESIVKSLA TEMTIVANEL AKHQGRQTLG AGDFRTALAV ...String:
MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMSQIDEH VTEMTEFEAE HESTYSEHSD EEEQELGARV PSRKQKGKAA AKKVKKAVAK KSGEERRRKK NYDSFATFIA KLVGPNGKGR KPGFSAKGME VLESIVKSLA TEMTIVANEL AKHQGRQTLG AGDFRTALAV RGSLIAREPA TVKALTEMGE KAVLKYQSSL GRPAKTAPKK KKATKKASA

-
Macromolecule #5: WIDOM 601 DNA (207 MER) strand 1

MacromoleculeName: WIDOM 601 DNA (207 MER) strand 1 / type: dna / ID: 5 / Details: 5' - 3', double stranded / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString: ATCGGACCCT ATCGCGAGCC AGGCCTGAGA ATCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAACCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCCAGGC ...String:
ATCGGACCCT ATCGCGAGCC AGGCCTGAGA ATCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAACCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCCAGGC CTTGTGTCGC GAAATTCATA TTAATTAATA CTAGAT

-
Macromolecule #6: WIDOM 601 DNA (207 MER) Strand 2

MacromoleculeName: WIDOM 601 DNA (207 MER) Strand 2 / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString: ATCTAGTATT AATTAATATG AATTTCGCGA CACAAGGCCT GGATGTATAT ATCTGACACG TGCCTGGAG ACTAGGGAGT AATCCCCTTG GCGGTTAAAA CGCGGGGGAC AGCGCGTACG T GCGTTTAA GCGGTGCTAG AGCTGTCTAC GACCAATTGA GCGGCCTCGG ...String:
ATCTAGTATT AATTAATATG AATTTCGCGA CACAAGGCCT GGATGTATAT ATCTGACACG TGCCTGGAG ACTAGGGAGT AATCCCCTTG GCGGTTAAAA CGCGGGGGAC AGCGCGTACG T GCGTTTAA GCGGTGCTAG AGCTGTCTAC GACCAATTGA GCGGCCTCGG CACCGGATTC TC AGGCCTG GCTCGCGATA GGGTCCGAT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium Chloride
20.0 mMTris-Hydrochloric acid
5.0 mMDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72768
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