[English] 日本語
Yorodumi
- EMDB-11102: HDAC-PC-Nuc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11102
TitleHDAC-PC-Nuc
Map dataHDAC-PC-Nuc
Sample
  • Complex: HDAC-PC-Nuc
    • Complex: Histone deacetylase
      • Protein or peptide: x 4 types
    • Complex: Histone
      • Protein or peptide: x 8 types
    • Complex: DNA
      • DNA: x 2 types
  • Ligand: x 1 types
KeywordsProtein complex / GENE REGULATION
Function / homology
Function and homology information


HDA1 complex / : / HSF1 activation / HDACs deacetylate histones / nucleosome array spacer activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / regulatory ncRNA-mediated gene silencing / SUMOylation of chromatin organization proteins / histone deacetylase complex ...HDA1 complex / : / HSF1 activation / HDACs deacetylate histones / nucleosome array spacer activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / regulatory ncRNA-mediated gene silencing / SUMOylation of chromatin organization proteins / histone deacetylase complex / epigenetic regulation of gene expression / chromosome segregation / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / protein heterodimerization activity / 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 / nucleoplasm / 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 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B / Histone H2B / Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone deacetylase HDA1 / Histone H4 / Histone H3.2 / HDA1 complex subunit 3 / HDA1 complex subunit 2 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / unidentified plasmid (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsLee J-H / Bollschweiler D
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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6z6p
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11102.png

Downloads & links

-
Map

FileDownload / File: emd_11102.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHDAC-PC-Nuc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 540 pix.
= 459.648 Å		0.85 Å/pix.
x 540 pix.
= 459.648 Å		0.85 Å/pix.
x 540 pix.
= 459.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.04
Minimum - Maximum-0.06135045 - 0.27088946
Average (Standard dev.)-0.00038719067 (±0.008378092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 459.64798 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85120.85120.8512
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z459.648459.648459.648
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS540540540
D min/max/mean-0.0610.271-0.000

-
Supplemental data

-
Sample components

+
Entire : HDAC-PC-Nuc

EntireName: HDAC-PC-Nuc
Components
  • Complex: HDAC-PC-Nuc
    • Complex: Histone deacetylase
      • Protein or peptide: Histone deacetylase HDA1
      • Protein or peptide: Histone deacetylase HDA1
      • Protein or peptide: HDA1 complex subunit 3,HDA1 complex subunit 3
      • Protein or peptide: HDA1 complex subunit 2
    • Complex: Histone
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (145-MER)
      • DNA: DNA (145-MER)
  • Ligand: ZINC ION

+
Supramolecule #1: HDAC-PC-Nuc

SupramoleculeName: HDAC-PC-Nuc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14

+
Supramolecule #2: Histone deacetylase

SupramoleculeName: Histone deacetylase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#12
Source (natural)Organism: Xenopus laevis (African clawed frog)

+
Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #13-#14
Source (natural)Organism: unidentified plasmid (others)

+
Macromolecule #1: Histone deacetylase HDA1

MacromoleculeName: Histone deacetylase HDA1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

UniProtKB: Histone deacetylase HDA1

+
Macromolecule #2: Histone deacetylase HDA1

MacromoleculeName: Histone deacetylase HDA1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

UniProtKB: Histone deacetylase HDA1

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

MacromoleculeName: HDA1 complex subunit 3,HDA1 complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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

UniProtKB: HDA1 complex subunit 3, HDA1 complex subunit 3

+
Macromolecule #4: HDA1 complex subunit 2

MacromoleculeName: HDA1 complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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

UniProtKB: HDA1 complex subunit 2

+
Macromolecule #5: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.431358 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEASE AYLVALFEDT NLCAIHAKRV TIMPKDIQL ARRIRGER

UniProtKB: Histone H3

+
Macromolecule #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 9.409056 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

+
Macromolecule #7: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.294136 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRSSRAGLQF PVGRVHRLLR KGNYAERVGA GAPVYLAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQL AVRNDEELNK LLGRVTIAQ GGVLPNIQSV LLPK

UniProtKB: Histone H2A

+
Macromolecule #8: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.607212 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSAK

UniProtKB: Histone H2B

+
Macromolecule #9: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.405321 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HRYRPGTVAL REIRRYQKST ELLIRKLPFQ RLVREIAQDF KTDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLA RRIRGERA

UniProtKB: Histone H3.2

+
Macromolecule #10: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 8.795306 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NIQGITKPAI RRLARRGGVK RISGLIYEET RGVLKVFLEN VIRDAVTYTE HAKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

+
Macromolecule #11: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.494393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKTRSSRAGL QFPVGRVHRL LRKGNYAERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAVRNDEEL NKLLGRVTI AQGGVLPNIQ SVLLPK

UniProtKB: Histone H2A type 1

+
Macromolecule #12: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.348852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRKESYAIYV YKVLKQVHPD TGISSKAMSI MNSFVNDVFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSA

UniProtKB: Histone H2B

+
Macromolecule #13: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unidentified plasmid (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

+
Macromolecule #14: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unidentified plasmid (others)
Molecular weightTheoretical: 44.99166 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DG) (DA)(DT)

+
Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 77.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1) / Number images used: 41279
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

-
Atomic model buiding 1

DetailsReal space refinement
Output model

PDB-6z6p:
HDAC-PC-Nuc

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more