[English] 日本語
Yorodumi
- EMDB-15709: Structure of a nucleosome-bound MuvB transcription factor complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15709
TitleStructure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling
Map dataMMBcore:NCP overall refined map at 10 Angstrom resolution
Sample
  • Complex: MuvBcore:B-MYB complex with a 167bp nucleosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsAlfieri C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215458/Z/19/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling.
Authors: Marios G Koliopoulos / Reyhan Muhammad / Theodoros I Roumeliotis / Fabienne Beuron / Jyoti S Choudhary / Claudio Alfieri /
Abstract: Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors ...Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors B-MYB and FOXM1 activate mitotic genes during cell proliferation. The mechanisms of transcriptional regulation by these complexes are still poorly characterised. Here, we combine biochemical analysis and in vitro reconstitution, with structural analysis by cryo-electron microscopy and cross-linking mass spectrometry, to functionally examine these complexes. We find that the MuvB:B-MYB complex binds and remodels nucleosomes, thereby exposing nucleosomal DNA. This remodelling activity is supported by B-MYB which directly binds the remodelled DNA. Given the remodelling activity on the nucleosome, we propose that the MuvB:B-MYB complex functions as a pioneer transcription factor complex. In this work, we rationalise prior biochemical and cellular studies and provide a molecular framework of interactions on a protein complex that is key for cell cycle regulation.
History
DepositionSep 1, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15709.png

Downloads & links

-
Map

FileDownload / File: emd_15709.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMMBcore:NCP overall refined map at 10 Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.49 Å/pix.
x 100 pix.
= 348.84 Å		3.49 Å/pix.
x 100 pix.
= 348.84 Å		3.49 Å/pix.
x 100 pix.
= 348.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4884 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0505
Minimum - Maximum-0.043289997 - 0.28741992
Average (Standard dev.)-0.0004896084 (±0.011054545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 348.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: MMB:DNA local refined map at 7.5 Angstrom resolution, sharpened more

Fileemd_15709_additional_1.map
AnnotationMMB:DNA local refined map at 7.5 Angstrom resolution, sharpened more
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: MMB:DNA local refined map at 7.5 Angstrom resolution

Fileemd_15709_additional_2.map
AnnotationMMB:DNA local refined map at 7.5 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: NCP147 local refined map at 6.9 Angstrom resolution

Fileemd_15709_additional_3.map
AnnotationNCP147 local refined map at 6.9 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: LIN9CTD:NCP local refined map at 7.1 Angstrom resolution

Fileemd_15709_additional_4.map
AnnotationLIN9CTD:NCP local refined map at 7.1 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: MMBhead local refined map at 7.5 Angstrom resolution

Fileemd_15709_additional_5.map
AnnotationMMBhead local refined map at 7.5 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: NCP127 local refined map at 3.3 Angstrom resolution

Fileemd_15709_additional_6.map
AnnotationNCP127 local refined map at 3.3 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: LIN9:52CC local refined map at 8.7 Angstrom resolution

Fileemd_15709_additional_7.map
AnnotationLIN9:52CC local refined map at 8.7 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: MMBcore:NCP overall refined map at 10 Angstrom resolution

Fileemd_15709_half_map_1.map
AnnotationMMBcore:NCP overall refined map at 10 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: MMBcore:NCP overall refined map at 10 Angstrom resolution

Fileemd_15709_half_map_2.map
AnnotationMMBcore:NCP overall refined map at 10 Angstrom resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MuvBcore:B-MYB complex with a 167bp nucleosome

EntireName: MuvBcore:B-MYB complex with a 167bp nucleosome
Components
  • Complex: MuvBcore:B-MYB complex with a 167bp nucleosome

-
Supramolecule #1: MuvBcore:B-MYB complex with a 167bp nucleosome

SupramoleculeName: MuvBcore:B-MYB complex with a 167bp nucleosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 400 kDa/nm

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237061
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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://pdbjlvh1.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