[English] 日本語
Yorodumi
- EMDB-12453: Cryo-EM structure of the Lin28B nucleosome core particle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12453
TitleCryo-EM structure of the Lin28B nucleosome core particle
Map dataLin28B Nucleosome Core Particle
Sample
  • Complex: Lin28B Nucleosome Core Particle
    • Complex: Histone H3.1Histone H3
      • Protein or peptide: Histone H3.1Histone H3
    • Complex: Histone H4
      • Protein or peptide: Histone H4
    • Complex: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2A type 1-B/E
    • Complex: Histone H2B type 1-J
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA
      • DNA: DNA (131-MER)
      • DNA: DNA (131-MER)
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / regulation of gene expression, epigenetic / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway ...negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / regulation of gene expression, epigenetic / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / SUMOylation of chromatin organization proteins / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / heterochromatin assembly / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / lipopolysaccharide binding / Metalloprotease DUBs / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / nucleosome assembly / HDMs demethylate histones / HCMV Early Events / Pre-NOTCH Transcription and Translation / Meiotic recombination / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosome / UCH proteinases / DNA-templated transcription, initiation / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / killing of cells of another organism / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / cadherin binding / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein domain specific binding / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRoberts GA / Ozkan B / Gachulincova I / O Dwyer MR / Hall-Ponsele E / Saxena M / Robinson PJ / Soufi A
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N024028/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M0180404/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R008795/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M010996/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nat Cell Biol / Year: 2021
Title: Dissecting OCT4 defines the role of nucleosome binding in pluripotency.
Authors: Gareth A Roberts / Burak Ozkan / Ivana Gachulincová / Michael R O'Dwyer / Elisa Hall-Ponsele / Manoj Saxena / Philip J Robinson / Abdenour Soufi /
Abstract: Pioneer transcription factors such as OCT4 can target silent genes embedded in nucleosome-dense regions. How nucleosome interaction enables transcription factors to target chromatin and determine ...Pioneer transcription factors such as OCT4 can target silent genes embedded in nucleosome-dense regions. How nucleosome interaction enables transcription factors to target chromatin and determine cell identity remains elusive. Here, we systematically dissect OCT4 to show that nucleosome binding is encoded within the DNA-binding domain and yet can be uncoupled from free-DNA binding. Furthermore, accelerating the binding kinetics of OCT4 to DNA enhances nucleosome binding. In cells, uncoupling nucleosome binding diminishes the ability of OCT4 to individually access closed chromatin, while more dynamic nucleosome binding results in expansive genome scanning within closed chromatin. However, both uncoupling and enhancing nucleosome binding are detrimental to inducing pluripotency from differentiated cells. Remarkably, stable interactions between OCT4 and nucleosomes are continuously required for maintaining the accessibility of pluripotency enhancers in stem cells. Our findings reveal how the affinity and residence time of OCT4-nucleosome complexes modulate chromatin accessibility during cell fate changes and maintenance.
History
DepositionFeb 19, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00958
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00958
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nl0
  • Surface level: 0.00958
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_12453.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLin28B Nucleosome Core Particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 376 pix.
= 244.135 Å
0.65 Å/pix.
x 376 pix.
= 244.135 Å
0.65 Å/pix.
x 376 pix.
= 244.135 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6493 Å
Density
Contour LevelBy AUTHOR: 0.00958 / Movie #1: 0.00958
Minimum - Maximum-0.026079396 - 0.052641526
Average (Standard dev.)0.00010164618 (±0.0013425621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 244.13528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.649295212765960.649295212765960.64929521276596
M x/y/z376376376
origin x/y/z0.0000.0000.000
length x/y/z244.135244.135244.135
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS376376376
D min/max/mean-0.0260.0530.000

-
Supplemental data

-
Sample components

+
Entire : Lin28B Nucleosome Core Particle

EntireName: Lin28B Nucleosome Core Particle
Components
  • Complex: Lin28B Nucleosome Core Particle
    • Complex: Histone H3.1Histone H3
      • Protein or peptide: Histone H3.1Histone H3
    • Complex: Histone H4
      • Protein or peptide: Histone H4
    • Complex: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2A type 1-B/E
    • Complex: Histone H2B type 1-J
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA
      • DNA: DNA (131-MER)
      • DNA: DNA (131-MER)

+
Supramolecule #1: Lin28B Nucleosome Core Particle

SupramoleculeName: Lin28B Nucleosome Core Particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 209.739 KDa

+
Supramolecule #2: Histone H3.1

SupramoleculeName: Histone H3.1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #3: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #4: Histone H2A type 1-B/E

SupramoleculeName: Histone H2A type 1-B/E / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #5: Histone H2B type 1-J

SupramoleculeName: Histone H2B type 1-J / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #6: DNA

SupramoleculeName: DNA / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

+
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: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

+
Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

+
Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

+
Macromolecule #5: DNA (131-MER)

MacromoleculeName: DNA (131-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.398344 KDa
SequenceString: (DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)(DA)(DC)(DT)(DT)(DA) ...String:
(DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)(DA)(DC)(DT)(DT)(DA)(DC)(DT) (DC)(DC)(DA)(DA)(DC)(DA)(DA)(DT)(DA)(DC) (DA)(DG) (DA)(DT)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DA)(DA)(DT)(DG)(DT)(DA)(DG) (DT)(DC)(DT) (DA)(DA)(DG)(DT)(DG)(DA) (DA)(DG)(DG)(DA)(DA)(DG)(DA)(DA)(DG)(DG) (DA)(DA)(DA)(DG) (DG)(DT)(DG)(DG)(DG) (DA)(DG)(DC)(DT)(DG)(DC)(DC)(DA)(DT)(DC) (DA)(DC)(DT)(DC)(DA) (DG)(DA)(DA)(DT) (DT)(DG)(DT)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DG)(DG)(DA)(DT)(DT)(DG) (DT)(DG)(DC) (DA)(DA)(DG)(DC)(DT)(DT)(DG)(DT)(DG)(DA) (DA)(DT)(DA)(DA)(DA)(DG)(DA) (DC)(DA)

+
Macromolecule #6: DNA (131-MER)

MacromoleculeName: DNA (131-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.59568 KDa
SequenceString: (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DA) (DT) (DT)(DC)(DT)(DG)(DA)(DG) ...String:
(DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DA) (DT) (DT)(DC)(DT)(DG)(DA)(DG)(DT)(DG) (DA)(DT)(DG)(DG)(DC)(DA)(DG)(DC)(DT)(DC) (DC)(DC) (DA)(DC)(DC)(DT)(DT)(DT)(DC) (DC)(DT)(DT)(DC)(DT)(DT)(DC)(DC)(DT)(DT) (DC)(DA)(DC) (DT)(DT)(DA)(DG)(DA)(DC) (DT)(DA)(DC)(DA)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DG)(DC) (DA)(DT)(DC)(DT)(DG) (DT)(DA)(DT)(DT)(DG)(DT)(DT)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DG) (DT)(DT)(DC)(DC) (DA)(DT)(DG)(DT)(DT)(DA)(DA)(DT)(DA)(DC) (DT)(DC)(DA)(DC)(DC)(DA) (DC)(DT)(DG) (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DG)(DT)(DT) (DA)(DA)(DT)(DA)(DC)(DC)(DA) (DC)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.7045 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 217170
FSC plot (resolution estimation)

+
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