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- EMDB-14239: Structure of MuvB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14239
TitleStructure of MuvB complex
Map data
Sample
  • Complex: MuvB complex
    • Protein or peptide: Protein lin-9 homolog
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Protein lin-37 homolog
Function / homology
Function and homology information


: / Myb complex / CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 ...: / Myb complex / CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / ATPase complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / DNA biosynthetic process / Sin3-type complex / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / transcription repressor complex / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / regulation of cell cycle / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein LIN37 / LIN37 / Protein LIN-9/Protein ALWAYS EARLY / DIRP domain / LIN-9, C-terminal / DIRP / LIN9 C-terminal / DIRP / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex ...Protein LIN37 / LIN37 / Protein LIN-9/Protein ALWAYS EARLY / DIRP domain / LIN-9, C-terminal / DIRP / LIN9 C-terminal / DIRP / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Protein lin-9 homolog / Protein lin-37 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKoliopoulos MG / Alfieri C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215458/Z/19 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
DepositionFeb 2, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14239.png

Downloads & links

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Map

FileDownload / File: emd_14239.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 216 pix.
= 244.944 Å		1.13 Å/pix.
x 216 pix.
= 244.944 Å		1.13 Å/pix.
x 216 pix.
= 244.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.134 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.10030206 - 0.16857924
Average (Standard dev.)0.00012423107 (±0.002887711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 244.94398 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : MuvB complex

EntireName: MuvB complex
Components
  • Complex: MuvB complex
    • Protein or peptide: Protein lin-9 homolog
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Protein lin-37 homolog

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Supramolecule #1: MuvB complex

SupramoleculeName: MuvB complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightExperimental: 180 KDa

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Macromolecule #1: Protein lin-9 homolog

MacromoleculeName: Protein lin-9 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.03566 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAELDQLPDE SSSAKALVSL KEGSLSNTWN EKYSSLQKTP VWKGRNTSSA VEMPFRNSKR SRLFSDEDDR QINTRSPKRN QRVAMVPQK FTATMSTPDK KASQKIGFRL RNLLKLPKAH KWCIYEWFYS NIDKPLFEGD NDFCVCLKES FPNLKTRKLT R VEWGKIRR ...String:
MAELDQLPDE SSSAKALVSL KEGSLSNTWN EKYSSLQKTP VWKGRNTSSA VEMPFRNSKR SRLFSDEDDR QINTRSPKRN QRVAMVPQK FTATMSTPDK KASQKIGFRL RNLLKLPKAH KWCIYEWFYS NIDKPLFEGD NDFCVCLKES FPNLKTRKLT R VEWGKIRR LMGKPRRCSS AFFEEERSAL KQKRQKIRLL QQRKVADVSQ FKDLPDEIPL PLVIGTKVTA RLRGVHDGLF TG QIDAVDT LNATYRVTFD RTGLGTHTIP DYEVLSNEPH ETMPIAAFGQ KQRPSRFFMT PPRLHYTPPL QSPIIDNDPL LGQ SPWRSK ISGSDTETLG GFPVEFLIQV TRLSKILMIK KEHIKKLREM NTEAEKLKSY SMPISIEFQR RYATIVLELE QLNK DLNKV LHKVQQYCYE LAPDQGLQPA DQPTDMRRRC EEEAQEIVRH ANSSTGQPCV ENENLTDLIS RLTAILLQIK CLAEG GDLN SFEFKSLTDS LNDIKSTIDA SNISCFQNNV EIHVAHIQSG LSQMGNLHAF AANNTNRD

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Macromolecule #2: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String:
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS

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Macromolecule #3: Protein lin-37 homolog

MacromoleculeName: Protein lin-37 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.37524 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MFPVKVKVEK SELEMAKARN QLDAVLQCLL EKSHMDRERL DEEAGKTPSD THNKDCSIAA TGKRPSARFP HQRRKKRREM DDGLAEGGP QRSNTYVIKL FDRSVDLAQF SENTPLYPIC RAWMRNSPSV RERECSPSSP LPPLPEDEEG SEVTNSKSRD V YKLPPPTP ...String:
MFPVKVKVEK SELEMAKARN QLDAVLQCLL EKSHMDRERL DEEAGKTPSD THNKDCSIAA TGKRPSARFP HQRRKKRREM DDGLAEGGP QRSNTYVIKL FDRSVDLAQF SENTPLYPIC RAWMRNSPSV RERECSPSSP LPPLPEDEEG SEVTNSKSRD V YKLPPPTP PGPPGDACRS RIPSPLQPEM QGTPDDEPSE PEPSPSTLIY RNMQRWKRIR QRWKEASHRN QLRYSESMKI LR EMYERQG SALEVLFQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26641

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