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- EMDB-11837: Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11837
TitleStructure of the MTA1/HDAC1/MBD2 NURD deacetylase complex
Map dataNuRD deacetylase complex
Sample
  • Complex: NuRD deacetylase complex containing two copies of MTA1 and HDAC1 and a single copy of MBD2
    • Protein or peptide: Methyl-CpG-binding domain protein 2
    • Protein or peptide: Metastasis-associated protein MTA1
    • Protein or peptide: Histone deacetylase 1
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION
KeywordsDeacetylase / Complex / TRANSCRIPTION
Function / homology
Function and homology information


Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / satellite DNA binding / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / negative regulation of androgen receptor signaling pathway / ventricular cardiac muscle tissue development ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / satellite DNA binding / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / negative regulation of androgen receptor signaling pathway / ventricular cardiac muscle tissue development / fungiform papilla formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / maternal behavior / siRNA binding / regulation of stem cell differentiation / protein deacetylation / Regulation of MITF-M-dependent genes involved in apoptosis / STAT3 nuclear events downstream of ALK signaling / Transcription of E2F targets under negative control by DREAM complex / histone deacetylase / positive regulation of protein autoubiquitination / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / protein lysine deacetylase activity / positive regulation of signaling receptor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / histone deacetylase activity / response to ionizing radiation / positive regulation of oligodendrocyte differentiation / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / Notch-HLH transcription pathway / entrainment of circadian clock by photoperiod / eyelid development in camera-type eye / Sin3-type complex / E-box binding / cellular response to platelet-derived growth factor stimulus / locomotor rhythm / oligodendrocyte differentiation / odontogenesis of dentin-containing tooth / RNA Polymerase I Transcription Initiation / SUMOylation of transcription factors / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / G0 and Early G1 / cellular response to organic cyclic compound / NF-kappaB binding / positive regulation of Wnt signaling pathway / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / embryonic organ development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of intrinsic apoptotic signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / heterochromatin / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of canonical NF-kappaB signal transduction / MECP2 regulates neuronal receptors and channels / response to mechanical stimulus / Regulation of TP53 Activity through Acetylation / transcription repressor complex / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / response to nutrient levels / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / promoter-specific chromatin binding / hippocampus development / Deactivation of the beta-catenin transactivating complex / positive regulation of smooth muscle cell proliferation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / heterochromatin formation / neuron differentiation / Wnt signaling pathway / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants
Similarity search - Function
Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type ...Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone deacetylase / 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 / : / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / DNA-binding domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Ureohydrolase domain superfamily / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Metastasis-associated protein MTA1 / Histone deacetylase 1 / Methyl-CpG-binding domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsMillard CJ / Fairall L
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome TrustWT100237/Z/12/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17136 United Kingdom
Wolfson Foundation United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2020
Title: The topology of chromatin-binding domains in the NuRD deacetylase complex.
Authors: Christopher J Millard / Louise Fairall / Timothy J Ragan / Christos G Savva / John W R Schwabe /
Abstract: Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated ...Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate.
History
DepositionOct 14, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ao8
  • Surface level: 0.01
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11837.png

Downloads & links

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Map

FileDownload / File: emd_11837.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNuRD deacetylase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.010286578 - 0.042806547
Average (Standard dev.)0.00013374453 (±0.0012437036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z327.000327.000327.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0100.0430.000

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Supplemental data

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Mask #1

Fileemd_11837_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: NuRD deacetylase complex - half2

Fileemd_11837_half_map_1.map
AnnotationNuRD deacetylase complex - half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: NuRD deacetylase complex - half1

Fileemd_11837_half_map_2.map
AnnotationNuRD deacetylase complex - half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NuRD deacetylase complex containing two copies of MTA1 and HDAC1 ...

EntireName: NuRD deacetylase complex containing two copies of MTA1 and HDAC1 and a single copy of MBD2
Components
  • Complex: NuRD deacetylase complex containing two copies of MTA1 and HDAC1 and a single copy of MBD2
    • Protein or peptide: Methyl-CpG-binding domain protein 2
    • Protein or peptide: Metastasis-associated protein MTA1
    • Protein or peptide: Histone deacetylase 1
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: NuRD deacetylase complex containing two copies of MTA1 and HDAC1 ...

SupramoleculeName: NuRD deacetylase complex containing two copies of MTA1 and HDAC1 and a single copy of MBD2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Methyl-CpG-binding domain protein 2

MacromoleculeName: Methyl-CpG-binding domain protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.323625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRAHPGGGRC CPEQEEGESA AGGSGAGGDS AIEQGGQGSA LAPSPVSGVR REGARGGGRG RGRWKQAGRG GGVCGRGRGR GRGRGRGRG RGRGRGRPPS GGSGLGGDGG GCGGGGSGGG GAPRREPVPF PSGSAGPGPR GPRATESGKR MDCPALPPGW K KEEVIRKS ...String:
MRAHPGGGRC CPEQEEGESA AGGSGAGGDS AIEQGGQGSA LAPSPVSGVR REGARGGGRG RGRWKQAGRG GGVCGRGRGR GRGRGRGRG RGRGRGRPPS GGSGLGGDGG GCGGGGSGGG GAPRREPVPF PSGSAGPGPR GPRATESGKR MDCPALPPGW K KEEVIRKS GLSAGKSDVY YFSPSGKKFR SKPQLARYLG NTVDLSSFDF RTGKMMPSKL QKNKQRLRND PLNQNKGKPD LN TTLPIRQ TASIFKQPVT KVTNHPSNKV KSDPQRMNEQ PRQLFWEKRL QGLSASDVTE QIIKTMELPK GLQGVGPGSN DET LLSAVA SALHTSSAPI TGQVSAAVEK NPAVWLNTSQ PLCKAFIVTD EDIRKQEERV QQVRKKLEEA LMADILSRAA DTEE MDIEM DSGDEA

UniProtKB: Methyl-CpG-binding domain protein 2

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Macromolecule #2: Metastasis-associated protein MTA1

MacromoleculeName: Metastasis-associated protein MTA1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.904312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAANMYRVGD YVYFENSSSN PYLIRRIEEL NKTANGNVEA KVVCFYRRRD ISSTLIALAD KHATLSVCYK AGPGADNGEE GEIEEEMEN PEMVDLPEKL KHQLRHRELF LSRQLESLPA THIRGKCSVT LLNETESLKS YLEREDFFFY SLVYDPQQKT L LADKGEIR ...String:
MAANMYRVGD YVYFENSSSN PYLIRRIEEL NKTANGNVEA KVVCFYRRRD ISSTLIALAD KHATLSVCYK AGPGADNGEE GEIEEEMEN PEMVDLPEKL KHQLRHRELF LSRQLESLPA THIRGKCSVT LLNETESLKS YLEREDFFFY SLVYDPQQKT L LADKGEIR VGNRYQADIT DLLKEGEEDG RDQSRLETQV WEAHNPLTDK QIDQFLVVAR SVGTFARALD CSSSVRQPSL HM SAAAASR DITLFHAMDT LHKNIYDISK AISALVPQGG PVLCRDEMEE WSASEANLFE EALEKYGKDF TDIQQDFLPW KSL TSIIEY YYMWKTTDRY VQQKRLKAAE AESKLKQVYI PNYNKPNPNQ ISVNNVKAGV VNGTGAPGQS PGAGRACESC YTTQ SYQWY SWGPPNMQCR LCASCWTYWK KYGGLKMPTR LDGERPGPNR SNMSPHGLPA RSSGSPKFAM KTRQAFYLHT TKLTR IARR LCREILRPWH AARHPYLPIN SAAIKAECTA RLPEASQSPL VLKQAVRKPL EAVLRYLETH PRPPKPDPVK SVSSVL SSL TPAKVAPVIN NGSPTILGKR SYEQHNGVDG NMKKRLLMPS RGLANHGQAR HMGPSRNLLL NGKSYPTKVR LIRGGSL PP VKRRRMNWID APDDVFYMAT EETRKIRKLL SSSETKRAAR RPYKPIALRQ SQALPPRPPP PAPVNDEPIV IED

UniProtKB: Metastasis-associated protein MTA1

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Macromolecule #3: Histone deacetylase 1

MacromoleculeName: Histone deacetylase 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.178906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ ...String:
MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ RVLYIDIDIH HGDGVEEAFY TTDRVMTVSF HKYGEYFPGT GDLRDIGAGK GKYYAVNYPL RDGIDDESYE AI FKPVMSK VMEMFQPSAV VLQCGSDSLS GDRLGCFNLT IKGHAKCVEF VKSFNLPMLM LGGGGYTIRN VARCWTYETA VAL DTEIPN ELPYNDYFEY FGPDFKLHIS PSNMTNQNTN EYLEKIKQRL FENLRMLPHA PGVQMQAIPE DAIPEESGDE DEDD PDKRI SICSSDKRIA CEEEFSDSEE EGEGGRKNSS NFKKAKRVKT EDEKEKDPEE KKEVTEEEKT KEEKPEAKGV KEEVK LA

UniProtKB: Histone deacetylase 1

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Macromolecule #4: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHEPES
75.0 mMPotassium acetate
0.5 mMTCEP
0.1 %Glutaraldehyde
50.0 mMTris-HCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Details: 40 mA for 120 sec
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 3 seconds, blot force 10.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 15086 / Average exposure time: 5.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 324135
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5icn

Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 94041
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5icn

source_name: PDB, initial_model_type: experimental model

2ky8

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7ao8:
Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex

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