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- EMDB-3577: MTA2-RBBP7 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3577
TitleMTA2-RBBP7 complex
Map data
Sample
  • Complex: MTA2-RBBP7 complex
    • Other: MTA2-RBBP7 complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 38.0 Å
AuthorsBrasen C / Dorosz J / Wiuf A / Boesen T / Mirza O / Gajhede M
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2017
Title: Expression, purification and characterization of the human MTA2-RBBP7 complex.
Authors: Christoffer Brasen / Jerzy Dorosz / Anders Wiuf / Thomas Boesen / Osman Mirza / Michael Gajhede /
Abstract: The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and ...The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and plays important roles in regulating gene transcription, DNA damage repair and chromatin assembly. The complex is composed of six subunits: Metastasis Associated proteins MTA1/2/3 initially recruit histone chaperones RBBP4/7 followed by the histone deacetylases HDAC1/2 forming a core complex. Further association of the CpG-binding protein MBD2/3, p66α/β and the ATP-dependent helicase CDH3/4 constitutes the NuRD complex. Recent structural studies on truncated human proteins or orthologous have revealed that the stoichiometry of the MTA1-RBBP4 complex is 2:4. This study reports expression and purification of the intact human MTA2-RBBP7 complex using HEK293F cells as expression system. In analogy with findings on the Drosophila NuRD complex, we find that also the human MTA-RBBP can be isolated in vitro. Taken together with previous findings this suggests, that MTA-RBBP is a stable complex, with a central role in the initial assembly of the human NuRD complex. Refined 3D volumes of the complex generated from negative stain electron microscopy (EM) data reveals an elongated architecture that is capable of hinge like motion around the center of the particle.
History
DepositionJan 17, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMay 3, 2017-
UpdateMay 3, 2017-
Current statusMay 3, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3577.png

Downloads & links

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Map

FileDownload / File: emd_3577.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.15 Å
Density
Contour LevelBy EMDB: 0.005 / Movie #1: 0.02
Minimum - Maximum-0.032571185 - 0.10222287
Average (Standard dev.)0.00017141107 (±0.0044833473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 535.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.153.153.15
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z535.500535.500535.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170170
D min/max/mean-0.0330.1020.000

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Supplemental data

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Sample components

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Entire : MTA2-RBBP7 complex

EntireName: MTA2-RBBP7 complex
Components
  • Complex: MTA2-RBBP7 complex
    • Other: MTA2-RBBP7 complex

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Supramolecule #1: MTA2-RBBP7 complex

SupramoleculeName: MTA2-RBBP7 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pOPINHALO7/pOPINF

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Macromolecule #1: MTA2-RBBP7 complex

MacromoleculeName: MTA2-RBBP7 complex / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAANMYRVGD YVYFENSSSN PYLVRRIEEL NKTANGNVEA KVVCLFRRRD ISSSLNSLAD SNAREFEEE SKQPGVSEQQ RHQLKHRELF LSRQFESLPA THIRGKCSVT LLNETDILSQ Y LEKEDCFF YSLVFDPVQK TLLADQGEIR VGCKYQAEIP DRLVEGESDN ...String:
MAANMYRVGD YVYFENSSSN PYLVRRIEEL NKTANGNVEA KVVCLFRRRD ISSSLNSLAD SNAREFEEE SKQPGVSEQQ RHQLKHRELF LSRQFESLPA THIRGKCSVT LLNETDILSQ Y LEKEDCFF YSLVFDPVQK TLLADQGEIR VGCKYQAEIP DRLVEGESDN RNQQKMEMKV WD PDNPLTD RQIDQFLVVA RAVGTFARAL DCSSSIRQPS LHMSAAAASR DITLFHAMDT LQR NGYDLA KAMSTLVPQG GPVLCRDEME EWSASEAMLF EEALEKYGKD FNDIRQDFLP WKSL ASIVQ FYYMWKTTDR YIQQKRLKAA EADSKLKQVY IPTYTKPNPN QIISVGSKPG MNGAG FQKG LTCESCHTTQ SAQWYAWGPP NMQCRLCASC WIYWKKYGGL KTPTQLEGAT RGTTEP HSR GHLSRPEAQS LSPYTTSANR AKLLAKNRQT FLLQTTKLTR LARRMCRDLL QPRRAAR RP YAPINANAIK AECSIRLPKA AKTPLKIHPL VRLPLATIVK DLVAQAPLKP KTPRGTKT P INRNQLSQNR GLGGIMVKRA YETMAGAGVP FSANGRPLAS GIRSSSQPAA KRQKLNPAD APNPVVFVAT KDTRALRKAL THLEMRRAAR RPNLPLKVKP TLIAVRPPVP LPAPSHPAST NEPIVLED MASKEMFEDT VEERVINEEY KIWKKNTPFL YDLVMTHALQ WPSLTVQWLP EVTKPEGKDY ALHWLVLGT HTSDEQNHLV VARVHIPNDD AQFDASHCDS DKGEFGGFGS VTGKIECEIK I NHEGEVNR ARYMPQNPHI IATKTPSSDV LVFDYTKHPA KPDPSGECNP DLRLRGHQKE GY GLSWNSN LSGHLLSASD DHTVCLWDIN AGPKEGKIVD AKAIFTGHSA VVEDVAWHLL HES LFGSVA DDQKLMIWDT RSNTTSKPSH LVDAHTAEVN CLSFNPYSEF ILATGSADKT VALW DLRNL KLKLHTFESH KDEIFQVHWS PHNETILASS GTDRRLNVWD LSKIGEEQSA EDAED GPPE LLFIHGGHTA KISDFSWNPN EPWVICSVSE DNIMQIWQMA ENIYNDEESD VTTSEL EGQ GS
Recombinant expressionOrganism: Homo sapiens (human)

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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

BufferpH: 7.5
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 10.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1267

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