[English] 日本語
Yorodumi
- EMDB-29837: Human Oct4 bound to nucleosome with human nMatn1 sequence (focuse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29837
TitleHuman Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome)
Map datanMatn1 nucleosome
Sample
  • Complex: Nucleosome with Human nMatn1 sequence
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: nMatn1 DNA (top stand)
    • DNA: nMatn1 DNA (bottom strand)
KeywordsOct4 / Nucleosome / Histone / nMatn1 DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Xenopus laevis laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsSinha KK / Bilokapic S / Du Y / Malik D / Halic M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM135599-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM141694-01 United States
CitationJournal: Nature / Year: 2023
Title: Histone modifications regulate pioneer transcription factor cooperativity.
Authors: Kalyan K Sinha / Silvija Bilokapic / Yongming Du / Deepshikha Malik / Mario Halic /
Abstract: Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation ...Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming. However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.
History
DepositionFeb 17, 2023-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29837.png

Downloads & links

-
Map

FileDownload / File: emd_29837.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationnMatn1 nucleosome
Voxel sizeX=Y=Z: 0.805 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.03642948 - 0.08113043
Average (Standard dev.)0.0000074522695 (±0.0018464059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_29837_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29837_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nucleosome with Human nMatn1 sequence

EntireName: Nucleosome with Human nMatn1 sequence
Components
  • Complex: Nucleosome with Human nMatn1 sequence
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: nMatn1 DNA (top stand)
    • DNA: nMatn1 DNA (bottom strand)

-
Supramolecule #1: Nucleosome with Human nMatn1 sequence

SupramoleculeName: Nucleosome with Human nMatn1 sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

-
Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Details: Histone H3.2|Xenopus laevis / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

-
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Details: Histone H4|Xenopus laevis / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

-
Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

-
Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Details: Histone H2B 1.1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

-
Macromolecule #5: nMatn1 DNA (top stand)

MacromoleculeName: nMatn1 DNA (top stand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.93359 KDa
SequenceString: (DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DT)(DA)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DG) (DG) (DT)(DT)(DA)(DA)(DT)(DA) ...String:
(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DT)(DA)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DG) (DG) (DT)(DT)(DA)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA)(DC)(DA) (DC)(DA) (DC)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DA) (DC)(DA)(DC)(DA)(DT)(DA) (DT)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DT)(DG) (DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DC) (DA)(DC)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG) (DC)(DG)(DC)(DA)(DC)(DA) (DT)(DA)(DG) (DT)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DT) (DG)(DC)(DA)(DC)(DA)(DC)(DA) (DT)(DT) (DA)(DG)(DC)(DA)(DT)(DA)(DT)(DG)(DC)(DA) (DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DC) (DA)(DT)(DG)(DC)(DA)

-
Macromolecule #6: nMatn1 DNA (bottom strand)

MacromoleculeName: nMatn1 DNA (bottom strand) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.889855 KDa
SequenceString: (DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DT)(DA) (DT)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG) (DT)(DG)(DA)(DC)(DT)(DA) ...String:
(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DT)(DA) (DT)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG) (DT)(DG)(DA)(DC)(DT)(DA)(DT)(DG) (DT)(DG)(DC)(DG)(DC)(DA)(DT)(DG)(DC)(DA) (DT)(DG) (DT)(DG)(DC)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DA)(DT) (DA)(DC)(DG) (DT)(DG)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DA) (DT)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT) (DG)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DG) (DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DA)(DT)(DA) (DT)(DA)(DT) (DT)(DA)(DA)(DC)(DC)(DT)(DG)(DT)(DG)(DT) (DG)(DC)(DA)(DT)(DT)(DG)(DT) (DG)(DT) (DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT)(DT)(DA) (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG) (DC)(DA)(DT)(DG)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
1.0 mMC4H10O2S2DTT

Details: 50 mM HEPES pH 7.5, 1 mM DTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21970

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 450000

+
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