[English] 日本語
Yorodumi
- EMDB-46547: 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46547
Title147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde
Map data147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde
Sample
  • Complex: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with glutaraldehyde
    • Complex: 5S rDNA
      • DNA: 5S rDNA (noncoding strand)
      • DNA: 5S rDNA (coding strand)
    • Complex: Human core histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 2-A
      • Protein or peptide: Histone H2B type 1-M
Keywords5S rDNA nucleosome / natural nucleosome positioning sequence / glutaraldehyde / cross-linking / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / UCH proteinases / HCMV Early Events / structural constituent of chromatin / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / heterochromatin formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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
Similarity search - Domain/homology
Histone H4 / Histone H2A type 2-A / Histone H3.2 / Histone H2B type 1-M
Similarity search - Component
Biological speciesXenopus borealis (Kenyan clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAlegrio Louro J / Cruz-Becerra G / Kadonaga JT / Leschziner AE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM145296 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118060 United States
CitationJournal: Genes Dev / Year: 2025
Title: Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif.
Authors: Jaime Alegrio-Louro / Grisel Cruz-Becerra / George A Kassavetis / James T Kadonaga / Andres E Leschziner /
Abstract: The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally ...The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally determined. Here we used cryo-EM to show that both proteins bind to the nucleosome acidic patch via analogous arginine anchors with one molecule bound to each face of the nucleosome. We additionally used the natural promoter-containing 5S rDNA sequence for structural analysis of the nucleosome. These structures of an ancient nucleosome-binding motif suggest that there is an untapped realm of proteins with a related mode of binding to chromatin.
History
DepositionAug 11, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46547.png

Downloads & links

-
Map

FileDownload / File: emd_46547.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 208 pix.
= 194.48 Å		0.94 Å/pix.
x 208 pix.
= 194.48 Å		0.94 Å/pix.
x 208 pix.
= 194.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.98446345 - 1.4110543
Average (Standard dev.)0.0018680057 (±0.049523134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 194.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map B

Fileemd_46547_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_46547_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human...

EntireName: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with glutaraldehyde
Components
  • Complex: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with glutaraldehyde
    • Complex: 5S rDNA
      • DNA: 5S rDNA (noncoding strand)
      • DNA: 5S rDNA (coding strand)
    • Complex: Human core histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 2-A
      • Protein or peptide: Histone H2B type 1-M

-
Supramolecule #1: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human...

SupramoleculeName: Mono-nucleosome assembled with Xenopus borealis 5S rDNA and human histones, cross-linked with glutaraldehyde
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
Molecular weightTheoretical: 110 KDa

-
Supramolecule #2: 5S rDNA

SupramoleculeName: 5S rDNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)

-
Supramolecule #3: Human core histones

SupramoleculeName: Human core histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.775586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PGTVALREIR RYQKSTELLI RKLPFQRLVR EIAQDFKTDL RFQSSAVMAL QEASEAYLVG LFEDTNLCAI HAKRVTIMPK DIQLARRIR GERA

UniProtKB: Histone H3.2

-
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.853342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE TRGVLKVFLE NVIRDAVTYT EHAKRKTVTA MDVVYALKRQ GRTLYGFG

UniProtKB: Histone H4

-
Macromolecule #3: Histone H2A type 2-A

MacromoleculeName: Histone H2A type 2-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.26816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KSRSSRAGLQ FPVGRVHRLL RKGNYAERVG AGAPVYMAAV LEYLTAEILE LAGNAARDNK KTRIIPRHLQ LAIRNDEELN KLLGKVTIA QGGVLPNIQA VLLP

UniProtKB: Histone H2A type 2-A

-
Macromolecule #4: Histone H2B type 1-M

MacromoleculeName: Histone H2B type 1-M / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.876271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ESYSVYVYKV LKQVHPDTGI SSKAMGIMNS FVNDIFERIA GEASRLAHYN KRSTITSREI QTAVRLLLPG ELAKHAVSEG TKAVTKYTS

UniProtKB: Histone H2B type 1-M

-
Macromolecule #5: 5S rDNA (noncoding strand)

MacromoleculeName: 5S rDNA (noncoding strand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
Molecular weightTheoretical: 30.943762 KDa
SequenceString: (DG)(DA)(DA)(DA)(DA)(DG)(DA)(DC)(DC)(DC) (DT)(DG)(DG)(DC)(DA)(DT)(DG)(DG)(DG)(DG) (DA)(DG)(DG)(DA)(DG)(DC)(DT)(DG)(DG) (DG)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DA) (DG) (DA)(DA)(DG)(DG)(DC)(DA) ...String:
(DG)(DA)(DA)(DA)(DA)(DG)(DA)(DC)(DC)(DC) (DT)(DG)(DG)(DC)(DA)(DT)(DG)(DG)(DG)(DG) (DA)(DG)(DG)(DA)(DG)(DC)(DT)(DG)(DG) (DG)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DA) (DG) (DA)(DA)(DG)(DG)(DC)(DA)(DG)(DC) (DA)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DG) (DG)(DA) (DA)(DA)(DA)(DG)(DT)(DC)(DA) (DG)(DC)(DC)(DT)(DT)(DG)(DT)(DG)(DC)(DT) (DC)(DG)(DC) (DC)(DT)(DA)(DC)(DG)(DG) (DC)(DC)(DA)(DT)(DA)(DC)(DC)(DA)(DC)(DC) (DC)(DT)(DG)(DA)

GENBANK: GENBANK: V01426.1

-
Macromolecule #6: 5S rDNA (coding strand)

MacromoleculeName: 5S rDNA (coding strand) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus borealis (Kenyan clawed frog)
Molecular weightTheoretical: 30.76852 KDa
SequenceString: (DT)(DC)(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DT) (DA)(DT)(DG)(DG)(DC)(DC)(DG)(DT)(DA)(DG) (DG)(DC)(DG)(DA)(DG)(DC)(DA)(DC)(DA) (DA)(DG)(DG)(DC)(DT)(DG)(DA)(DC)(DT)(DT) (DT) (DT)(DC)(DC)(DT)(DC)(DC) ...String:
(DT)(DC)(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DT) (DA)(DT)(DG)(DG)(DC)(DC)(DG)(DT)(DA)(DG) (DG)(DC)(DG)(DA)(DG)(DC)(DA)(DC)(DA) (DA)(DG)(DG)(DC)(DT)(DG)(DA)(DC)(DT)(DT) (DT) (DT)(DC)(DC)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DT)(DG)(DC)(DT)(DG)(DC)(DC) (DT)(DT) (DC)(DT)(DG)(DG)(DG)(DG)(DG) (DG)(DG)(DG)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DC)(DC)(DT) (DC)(DC)(DC)(DC)(DA)(DT) (DG)(DC)(DC)(DA)(DG)(DG)(DG)(DT)(DC)(DT) (DT)(DT)(DT)(DC)

GENBANK: GENBANK: V01426.1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.13 mg/mL
BufferpH: 7.6
Component:
ConcentrationName
0.25 %Glutaraldehyde
23.0 mMHEPES-potassium
0.66 mMEDTA
77.0 mMPotassium chloride
0.0085 %(w/V)NP-40
32.0 mMSodium chloride
1.7 %(V/V)Glycerol
50.0 mMTris
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 5622 / Number real images: 5352 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware: (Name: cryoSPARC, RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53805
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab-initio job in cryoSPARC.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement job in cryoSPARC.
Final 3D classificationNumber classes: 10 / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9d3t:
147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde

+
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