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- EMDB-11094: HDAC-DC -

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Basic information

Entry
Database: EMDB / ID: EMD-11094
TitleHDAC-DC
Map dataHDAC-DC
Sample
  • Complex: HDAC-DC
    • Protein or peptide: Histone deacetylase HDA1
    • Protein or peptide: Histone deacetylase HDA1
    • Protein or peptide: HDA1 complex subunit 2
    • Protein or peptide: HDA1 complex subunit 3,HDA1 complex subunit 3
  • Ligand: ZINC ION
Function / homology
Function and homology information


HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / histone deacetylase / SUMOylation of chromatin organization proteins / regulatory ncRNA-mediated gene silencing / histone deacetylase activity / histone deacetylase complex / epigenetic regulation of gene expression ...HDA1 complex / negative regulation of transcription by transcription factor localization / HSF1 activation / HDACs deacetylate histones / histone deacetylase / SUMOylation of chromatin organization proteins / regulatory ncRNA-mediated gene silencing / histone deacetylase activity / histone deacetylase complex / epigenetic regulation of gene expression / chromosome segregation / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone deacetylase class II, yeast / Arb2 domain / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Arb2-like domain / Class II histone deacetylase complex subunits 2 and 3 / : / Histone deacetylase family / Histone deacetylase domain ...Histone deacetylase class II, yeast / Arb2 domain / HDA1 complex subunit 2/3 / HDA1 complex subunit 3 / HDA1 complex subunit 2/3 superfamily / Arb2-like domain / Class II histone deacetylase complex subunits 2 and 3 / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Histone deacetylase HDA1 / HDA1 complex subunit 3 / HDA1 complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.55 Å
AuthorsLee J-H / Bollschweiler D / Schaefer T / Huber R
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies.
Authors: Jung-Hoon Lee / Daniel Bollschweiler / Tillman Schäfer / Robert Huber /
Abstract: The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup ...The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda1-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.
History
DepositionMay 28, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z6h
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11094.png

Downloads & links

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Map

FileDownload / File: emd_11094.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHDAC-DC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 300 pix.
= 565.5 Å		1.89 Å/pix.
x 300 pix.
= 565.5 Å		1.89 Å/pix.
x 300 pix.
= 565.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.23140095 - 0.7539314
Average (Standard dev.)2.3958286e-05 (±0.033027258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 565.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8851.8851.885
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z565.500565.500565.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2310.7540.000

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Supplemental data

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Sample components

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Entire : HDAC-DC

EntireName: HDAC-DC
Components
  • Complex: HDAC-DC
    • Protein or peptide: Histone deacetylase HDA1
    • Protein or peptide: Histone deacetylase HDA1
    • Protein or peptide: HDA1 complex subunit 2
    • Protein or peptide: HDA1 complex subunit 3,HDA1 complex subunit 3
  • Ligand: ZINC ION

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Supramolecule #1: HDAC-DC

SupramoleculeName: HDAC-DC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone deacetylase HDA1

MacromoleculeName: Histone deacetylase HDA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 74.851953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RQVIVPVCMP KIHYSPLKTG LCYDVRMRYH AKIFTSYFEY IDPHPEDPRR IYRIYKILAE NGLINDPTLS GVDDLGDLML KIPVRAATS EEILEVHTKE HLEFIESTEK MSREELLKET EKGDSVYFNN DSYASARLPC GGAIEACKAV VEGRVKNSLA V VRPPGHHA ...String:
RQVIVPVCMP KIHYSPLKTG LCYDVRMRYH AKIFTSYFEY IDPHPEDPRR IYRIYKILAE NGLINDPTLS GVDDLGDLML KIPVRAATS EEILEVHTKE HLEFIESTEK MSREELLKET EKGDSVYFNN DSYASARLPC GGAIEACKAV VEGRVKNSLA V VRPPGHHA EPQAAGGFCL FSNVAVAAKN ILKNYPESVR RIMILDWDIH HGNGTQKSFY QDDQVLYVSL HRFEMGKYYP GT IQGQYDQ TGEGKGEGFN CNITWPVGGV GDAEYMWAFE QVVMPMGREF KPDLVIISSG FDAADGDTIG QCHVTPSCYG HMT HMLKSL ARGNLCVVLE GGYNLDAIAR SALSVAKVLI GEPPDELPDP LSDPKPEVIE MIDKVIRLQS KYWNCFRRRH ANSG CNFNE PINDSIISKN FPLQKAIRQQ QQHYLSDEFN FVTLPLVSMD LPDNTVLCTP NISESNTIII VVHDTSDIWA KRNVI SGTI DLSSSVIIDN SLDFIKWGLD RKYGIIDVNI PLTLFEPDNY SGMITSQEVL IYLWDNYIKY FPSVAKIAFI GIGDSY SGI VHLLGHRDTR AVTKTVINFL GDKQLKPLVP LVDETLSEWY FKNSLIFSNN SHQCWKENES RKPRKKFGRV LRCDTDG LN NIIEERFEEA TDFILDSFE

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Macromolecule #2: Histone deacetylase HDA1

MacromoleculeName: Histone deacetylase HDA1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 76.017211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENSLSTTSKS KRQVIVPVCM PKIHYSPLKT GLCYDVRMRY HAKIFTSYFE YIDPHPEDPR RIYRIYKILA ENGLINDPTL SGVDDLGDL MLKIPVRAAT SEEILEVHTK EHLEFIESTE KMSREELLKE TEKGDSVYFN NDSYASARLP CGGAIEACKA V VEGRVKNS ...String:
ENSLSTTSKS KRQVIVPVCM PKIHYSPLKT GLCYDVRMRY HAKIFTSYFE YIDPHPEDPR RIYRIYKILA ENGLINDPTL SGVDDLGDL MLKIPVRAAT SEEILEVHTK EHLEFIESTE KMSREELLKE TEKGDSVYFN NDSYASARLP CGGAIEACKA V VEGRVKNS LAVVRPPGHH AEPQAAGGFC LFSNVAVAAK NILKNYPESV RRIMILDWDI HHGNGTQKSF YQDDQVLYVS LH RFEMGKY YPGTIQGQYD QTGEGKGEGF NCNITWPVGG VGDAEYMWAF EQVVMPMGRE FKPDLVIISS GFDAADGDTI GQC HVTPSC YGHMTHMLKS LARGNLCVVL EGGYNLDAIA RSALSVAKVL IGEPPDELPD PLSDPKPEVI EMIDKVIRLQ SKYW NCFRR RHANSGCNFN EPINDSIISK NFPLQKAIRQ QQQHYLSDEF NFVTLPLVSM DLPDNTVLCT PNISESNTII IVVHD TSDI WAKRNVISGT IDLSSSVIID NSLDFIKWGL DRKYGIIDVN IPLTLFEPDN YSGMITSQEV LIYLWDNYIK YFPSVA KIA FIGIGDSYSG IVHLLGHRDT RAVTKTVINF LGDKQLKPLV PLVDETLSEW YFKNSLIFSN NSHQCWKENE SRKPRKK FG RVLRCDTDGL NNIIEERFEE ATDFILDSFE

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Macromolecule #3: HDA1 complex subunit 2

MacromoleculeName: HDA1 complex subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 71.915297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KVYYLPVTLT QFQKDLSEIL ISLHAKSFKA SIIGEPQADA VNKPSGLPAG PETHPYPTLS QRQLTYIFDS NIRAIANHPS LLVDHYMPR QLLRMEPTES SIAGSHKFQV LNQLINSICF RDREGSPNEV IKCAIIAHSI KELDLLEGLI LGKKFRTKRL S GTSLYNEK ...String:
KVYYLPVTLT QFQKDLSEIL ISLHAKSFKA SIIGEPQADA VNKPSGLPAG PETHPYPTLS QRQLTYIFDS NIRAIANHPS LLVDHYMPR QLLRMEPTES SIAGSHKFQV LNQLINSICF RDREGSPNEV IKCAIIAHSI KELDLLEGLI LGKKFRTKRL S GTSLYNEK HKFPNLPTVD STINKDGTPN SVSSTSSNSN STSYTGYSKD DYDYSVKRNL KKRKINTDDW LFLATTKHLK HD QYLLANY DIDMIISFDP MLEVELPALQ VLRNNANKDI PIIKLLVQNS PDHYLLDSEI KNSSVKSSHL SNNGHVDDSQ EYE EIKSSL LYFLQARNAP VNNCEIDYIK LVKCCLEGKD CNNILPVLDL ITLDEASKDS SDSGFWQPQL TKLQYSSTEL PLWD GPLDI KTYQTELMHR AVIRLRDIQD EYAKGTVPLY EKRLNETQRQ NQLDEIKNSV GLTFKKKQEV EKSINDSEKR LKHAM TEST KLQNKINHLL KNRQELENFN KLPSNTISSE NHLEEGSALA DKLKEYIDKN ATLFNKLKEL QQANAEKSKL NDELRS KYQ IESSKAAESA QTLKILQESM KSLENEVNGP LTKFSTESLK KELERLQNDF QSLKARNKFL KNYITL

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Macromolecule #4: HDA1 complex subunit 3,HDA1 complex subunit 3

MacromoleculeName: HDA1 complex subunit 3,HDA1 complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 63.422098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDYWLPTTM SLYQKELTDQ IVSLHYSDIL RYFETSHYKE DVILESMKTM CLNGSLVATH PYLLIDHYMP KSLITRDVPA HLAENSGKF SVLRDLINLV QEYETETAIV CRPGRTMDLL EALLLGNKVH IKRYDGHSIK SKQKANDFSC TVHLFSSEGI N FTKYPIKS ...String:
SGDYWLPTTM SLYQKELTDQ IVSLHYSDIL RYFETSHYKE DVILESMKTM CLNGSLVATH PYLLIDHYMP KSLITRDVPA HLAENSGKF SVLRDLINLV QEYETETAIV CRPGRTMDLL EALLLGNKVH IKRYDGHSIK SKQKANDFSC TVHLFSSEGI N FTKYPIKS KARFDMLICL DTTVDTSQKD IQYLLQYKRE RKGLERYAPI VRLVAINSID HCRLFFGKKF DKNSREYLEN VT AAMVILR DRLGTLPPDL RPIYSQKLHY LVEWLENPTV PWPLPDIYPL KQYTSMDVER SLLTEVHFKK NSSNVNYHLS SGI ITHKLI QSMGEVYMDI CVQKQELDDY SCLDDLQNDH LKFFSNEDEK IIKEYETVLR TNNENLNRSH ELEVENNLKF SQIE TLEKD IETLKGSLMA QGETLSKLKD AFVKTDNVQD EIEKEERVSV SRDTEKKYME QEIKRAVDAI RENEEETHKL NEKQN GLES ELKLKFEKSE ISTKELNEKI GFLKKELKLE NDLNEELVGQ LSKTMDNLEN LTIPRVRTQ

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 11396
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

DetailsReal space refinement
Output model

PDB-6z6h:
HDAC-DC

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