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- EMDB-3431: Negative Stain EM of NuRD subcomplex of RBBP4 and MTA1 (Human). -

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Basic information

Entry
Database: EMDB / ID: EMD-3431
TitleNegative Stain EM of NuRD subcomplex of RBBP4 and MTA1 (Human).
Map dataHuman MTA1 truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
Sample
  • Sample: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
  • Protein or peptide: Metastasis-associated protein MTA1 C-terminus (449-715)
  • Protein or peptide: Histone-binding protein RBBP4
KeywordsNuRD complex / RBBP4 / MTA1 / transcription regulation / chromatin / protein structure
Function / homology
Function and homology information


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 / positive regulation of protein autoubiquitination ...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 / positive regulation of protein autoubiquitination / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / response to ionizing radiation / negative regulation of gene expression, epigenetic / ATPase complex / entrainment of circadian clock by photoperiod / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / locomotor rhythm / SUMOylation of transcription factors / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / nucleosome assembly / transcription corepressor activity / nuclear envelope / double-strand break repair / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / histone binding / Potential therapeutics for SARS / transcription coactivator activity / DNA replication / chromosome, telomeric region / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / ELM2 domain ...Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Metastasis-associated protein MTA1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 29.7 Å
AuthorsSchmidberger JW / Sharif Tabar M / Torrado M / Silva APG / Landsberg MJ / Brilault L / Alqarni S / Zeng YC / Parker BL / Low JKK / Mackay JP
CitationJournal: Protein Sci / Year: 2016
Title: The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7.
Authors: Jason W Schmidberger / Mehdi Sharifi Tabar / Mario Torrado / Ana P G Silva / Michael J Landsberg / Lou Brillault / Saad AlQarni / Yi Cheng Zeng / Benjamin L Parker / Jason K K Low / Joel P Mackay /
Abstract: The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed ...The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4)2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex.
History
DepositionMay 9, 2016-
Header (metadata) releaseMay 18, 2016-
Map releaseMay 18, 2016-
UpdateAug 24, 2016-
Current statusAug 24, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.068
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.068
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3431.tif

Downloads & links

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Map

FileDownload / File: emd_3431.map.gz / Format: CCP4 / Size: 538.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman MTA1 truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.58 Å/pix.
x 52 pix.
= 290.16 Å		5.58 Å/pix.
x 52 pix.
= 290.16 Å		5.58 Å/pix.
x 52 pix.
= 290.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.068 / Movie #1: 0.068
Minimum - Maximum-0.31457576 - 0.4855015
Average (Standard dev.)-0.01756996 (±0.05386001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions525252
Spacing525252
CellA=B=C: 290.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.585.585.58
M x/y/z525252
origin x/y/z0.0000.0000.000
length x/y/z290.160290.160290.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS525252
D min/max/mean-0.3150.486-0.018

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Supplemental data

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Sample components

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Entire : Human MTA1 C-terminal truncation mutant (residues 449 to 715) bou...

EntireName: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
Components
  • Sample: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
  • Protein or peptide: Metastasis-associated protein MTA1 C-terminus (449-715)
  • Protein or peptide: Histone-binding protein RBBP4

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Supramolecule #1000: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bou...

SupramoleculeName: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4.
type: sample / ID: 1000
Oligomeric state: One copy of MTA1-C binds to two copies of RBBP4.
Number unique components: 2
Molecular weightExperimental: 130 KDa / Theoretical: 128 KDa / Method: SDS PAGE

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Macromolecule #1: Metastasis-associated protein MTA1 C-terminus (449-715)

MacromoleculeName: Metastasis-associated protein MTA1 C-terminus (449-715)
type: protein_or_peptide / ID: 1 / Name.synonym: MTA (449-715) / Number of copies: 1 / Oligomeric state: 1 X MTA1, 2 X RBBP4 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 30 KDa / Theoretical: 30 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 / Recombinant plasmid: pcDNA3.1
SequenceUniProtKB: Metastasis-associated protein MTA1

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Macromolecule #2: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 2 / Name.synonym: RBBP4 / Number of copies: 2 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 50 KDa / Theoretical: 48 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 / Recombinant plasmid: pcDNA3.1
SequenceUniProtKB: Histone-binding protein RBBP4

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 8.2 / Details: 50 mM HEPES KOH pH 8.2, 150 mM NaCl, 1 mM DTT.
StainingType: NEGATIVE
Details: After an incubation time of 5 min, the grid was blotted and washed with five drops of distilled water, blotted again and subsequently stained with a 2% (w/v) uranyl acetate solution for one ...Details: After an incubation time of 5 min, the grid was blotted and washed with five drops of distilled water, blotted again and subsequently stained with a 2% (w/v) uranyl acetate solution for one minute. Excess stain was then blotted away and the grid allowed to dry under air at ambient conditions.
GridDetails: Glow-discharged, carbon-coated 400-mesh copper grid (GSCu400CC ProSciTech)
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateDec 17, 2015
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 400
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 54000
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER

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Image processing

DetailsParticles were initially selected manually (1730 particles) then these were used to autopick 12114 particles using RELION. This was reduced to 9000 particles using manual inspection. Use of 2D class averaging reduced count to 4000 particles which were used to generate four 3D classes.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 4000
Final two d classificationNumber classes: 4
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4pby


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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