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- EMDB-64741: Cryo-EM structure of the histone deacetylase complex Rpd3L in com... -

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Entry
Database: EMDB / ID: EMD-64741
TitleCryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
Map data
Sample
  • Complex: Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
    • Protein or peptide: x 12 types
    • DNA: x 2 types
  • Protein or peptide: x 1 types
  • Ligand: x 1 types
KeywordsHistone deacetylase complex / Histone modification / Rpd3L / Cryo-EM / mono-nucleosome / GENE REGULATION/DNA / GENE REGULATION-DNA complex
Function / homology
Function and homology information


negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / positive regulation of inositol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / regulation of invasive growth in response to glucose limitation / conjugation with cellular fusion / PI5P Regulates TP53 Acetylation / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex ...negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / positive regulation of inositol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / regulation of invasive growth in response to glucose limitation / conjugation with cellular fusion / PI5P Regulates TP53 Acetylation / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / positive regulation of invasive growth in response to glucose limitation / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of reciprocal meiotic recombination / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / invasive growth in response to glucose limitation / Rpd3S complex / rDNA chromatin condensation / nucleophagy / SUMOylation of transcription cofactors / HDACs deacetylate histones / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / cell adhesion involved in single-species biofilm formation / histone H3K4me3 reader activity / histone deacetylase activity / negative regulation of transcription by RNA polymerase I / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / regulation of DNA-templated DNA replication initiation / Sin3-type complex / histone deacetylase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / Ub-specific processing proteases / nuclear periphery / meiotic cell cycle / transcription coregulator activity / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / histone deacetylase binding / structural constituent of chromatin / transcription corepressor activity / nucleosome / heterochromatin formation / nucleosome assembly / cellular response to heat / chromatin organization / response to oxidative stress / transcription coactivator activity / protein heterodimerization activity / cell division / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Histone deacetylation protein Rxt3 / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein RXT2, N-terminal / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 ...: / Histone deacetylation protein Rxt3 / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein RXT2, N-terminal / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 / Sds3-like / Sds3-like / Sds3-like / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / PhD finger domain / ING family / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / Histone deacetylase / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B 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 / Zinc finger, FYVE/PHD-type / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3 / Histone H2B / Transcriptional regulatory protein SIN3 / Transcriptional regulatory protein DEP1 / Histone deacetylase RPD3 / Transcriptional regulatory protein RXT2 / Transcriptional regulatory protein SAP30 / Transcriptional regulatory protein SDS3 / Transcriptional regulatory protein PHO23 / Histone H4 ...Histone H3 / Histone H2B / Transcriptional regulatory protein SIN3 / Transcriptional regulatory protein DEP1 / Histone deacetylase RPD3 / Transcriptional regulatory protein RXT2 / Transcriptional regulatory protein SAP30 / Transcriptional regulatory protein SDS3 / Transcriptional regulatory protein PHO23 / Histone H4 / Transcriptional regulatory protein RXT3 / Histone deacetylase complex subunit CTI6 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhao H / Li H / Wang C / Yang X / Zou B / Dong S / Zhang N / Zhou Y / Yi L / Zhang Y ...Zhao H / Li H / Wang C / Yang X / Zou B / Dong S / Zhang N / Zhou Y / Yi L / Zhang Y / Xie Y / Qin D / Chao W / Pei D / He J
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32361163669 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)32241021 China
Other government2023B1212060050
Other government2023B1212120009
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Chromatin context-dependent deacetylation by the asymmetric Rpd3L.
Authors: Heyu Zhao / Huadong Li / Chi Wang / Xuechen Yang / Binqian Zou / Shuqi Dong / Nan Zhang / Yuxing Zhou / Li Yi / Ying Zhang / Yixuan Xie / Dajiang Qin / William Chong Hang Chao / Duanqing Pei / Jun He /
Abstract: The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone ...The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase complex (HDAC) that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-electron microscopy structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.
History
DepositionMay 21, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64741.png

Downloads & links

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Map

FileDownload / File: emd_64741.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 600 pix.
= 426. Å		0.71 Å/pix.
x 600 pix.
= 426. Å		0.71 Å/pix.
x 600 pix.
= 426. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.021056697 - 0.5345006
Average (Standard dev.)0.0026408741 (±0.008543141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 426.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64741_msk_1.map
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Half map: #2

Fileemd_64741_half_map_1.map
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Half map: #1

Fileemd_64741_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the histone deacetylase complex Rpd3L in com...

EntireName: Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
Components
  • Complex: Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Transcriptional regulatory protein DEP1
    • Protein or peptide: Transcriptional regulatory protein SDS3
    • Protein or peptide: Transcriptional regulatory protein SAP30
    • Protein or peptide: Transcriptional regulatory protein RXT3
    • Protein or peptide: Transcriptional regulatory protein PHO23
    • Protein or peptide: Transcriptional regulatory protein RXT2
    • Protein or peptide: Histone deacetylase complex subunit CTI6
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • DNA: DNA (155-MER)
    • DNA: DNA (155-MER)
  • Protein or peptide: Histone deacetylase RPD3
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of the histone deacetylase complex Rpd3L in com...

SupramoleculeName: Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#15
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Transcriptional regulatory protein SIN3

MacromoleculeName: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 80.758352 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LNEEVTFFEK AKRYIGNKHL YTEFLKILNL YSQDILDLDD LVEKVDFYLG SNKELFTWFK NFVGYQEKTK CIENIVHEKH RLDLDLCEA FGPSYKRLPK SDTFMPCSGR DDMCWEVLND EWVGHPVWAS EDSGFIAHRK NQYEETLFKI EEERHEYDFY I ESNLRTIQ ...String:
LNEEVTFFEK AKRYIGNKHL YTEFLKILNL YSQDILDLDD LVEKVDFYLG SNKELFTWFK NFVGYQEKTK CIENIVHEKH RLDLDLCEA FGPSYKRLPK SDTFMPCSGR DDMCWEVLND EWVGHPVWAS EDSGFIAHRK NQYEETLFKI EEERHEYDFY I ESNLRTIQ CLETIVNKIE NMTENEKANF KLPPGLGHTS MTIYKKVIRK VYDKERGFEI IDALHEHPAV TAPVVLKRLK QK DEEWRRA QREWNKVWRE LEQKVFFKSL DHLGLTFKQA DKKLLTTKQL ISEISSIKVD QTNKKIHWLT PKPKSQLDFD FPD KNIFYD ILCLADTFIT HTTAYSNPDK ERLKDLLKYF ISLFFSISFE KIEESLYSHK QNVSESSGSD DGSSIASRKR PYQQ EMSLL DILHRSRYQK LKRSNDEDGK VPQLSEPPEE EPNTIEEEEL IDEEAKNPWL TGNLVEEANS QGIIQNRSIF NLFAN TNIY IFFRHWTTIY ERLLEIKQMN ERVTKEINTR STVTFAKDLD LLSSQLSEMG LDFVGEDAYK QVLRLSRRLI NGDLEH QWF EESLRQAYNN KAFKLYTIDK VTQSLVKHAH TLMTDAKTAE IMALFVKDRN ASTTSAKDQI IYRLQVRSHM SNTENMF RI EFDKRTLHVS IQYIALDDLT LKEPKADEDK WKYYVTSYAL P

UniProtKB: Transcriptional regulatory protein SIN3

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Macromolecule #2: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 43.524289 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DPITVKPSDK RRVAYFYDAD VGNYAYGAGH PMKPHRIRMA HSLIMNYGLY KKMEIYRAKP ATKQEMCQFH TDEYIDFLSR VTPDNLEMF KRESVKFNVG DDCPVFDGLY EYCSISGGGS MEGAARLNRG KCDVAVNYAG GLHHAKKSEA SGFCYLNDIV L GIIELLRY ...String:
DPITVKPSDK RRVAYFYDAD VGNYAYGAGH PMKPHRIRMA HSLIMNYGLY KKMEIYRAKP ATKQEMCQFH TDEYIDFLSR VTPDNLEMF KRESVKFNVG DDCPVFDGLY EYCSISGGGS MEGAARLNRG KCDVAVNYAG GLHHAKKSEA SGFCYLNDIV L GIIELLRY HPRVLYIDID VHHGDGVEEA FYTTDRVMTC SFHKYGEFFP GTGELRDIGV GAGKNYAVNV PLRDGIDDAT YR SVFEPVI KKIMEWYQPS AVVLQCGGDS LSGDRLGCFN LSMEGHANCV NYVKSFGIPM MVVGGGGYTM RNVARTWCFE TGL LNNVVL DKDLPYNEYY EYYGPDYKLS VRPSNMFNVN TPEYLDKVMT NIFANLENTK YAPSVQLNH

UniProtKB: Histone deacetylase RPD3

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Macromolecule #3: Transcriptional regulatory protein DEP1

MacromoleculeName: Transcriptional regulatory protein DEP1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 14.553604 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
EQRMTALKEI TDIEYKFAQL RQKLYDNQLV RLQTELQMCL EGSHPELQVY YSKIAAIRDY KLHRAYQRQK YELSCINTET IATRTFIHQ DFHKKVTDLR ARLLNRTTQT WYDINKERRD

UniProtKB: Transcriptional regulatory protein DEP1

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Macromolecule #4: Transcriptional regulatory protein SDS3

MacromoleculeName: Transcriptional regulatory protein SDS3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 35.851199 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: KDKRRFNIES KVNKIYQNFY SERDNQYKDR LTALQTDLTS LHQGDNGQYA RQVRDLEEER DLELVRLRLF EEYRVSRSGI EFQEDIEKA KAEHEKLIKL CKERLYSSIE QKIKKLQEER LLMDVANVHS YAMNYSRPQY QKNTRSHTVS GWDSSSNEYG R DTANESAT ...String:
KDKRRFNIES KVNKIYQNFY SERDNQYKDR LTALQTDLTS LHQGDNGQYA RQVRDLEEER DLELVRLRLF EEYRVSRSGI EFQEDIEKA KAEHEKLIKL CKERLYSSIE QKIKKLQEER LLMDVANVHS YAMNYSRPQY QKNTRSHTVS GWDSSSNEYG R DTANESAT DTGAGNDRRT LRRRNASKDT RGNNNNQDES DFQTGNGSGS NGHGSRQGSQ FPHFNNLTYK SGMNSDSDFL QG INEGTDL YAFLFGEKNP KDNANGNEKK KNRGAQRYST KTAPPLQSLK PDEVTEDISL IRELTGQPPA PFRL

UniProtKB: Transcriptional regulatory protein SDS3

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Macromolecule #5: Transcriptional regulatory protein SAP30

MacromoleculeName: Transcriptional regulatory protein SAP30 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 14.480324 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
RLTAAQQQYI KNLIETHITD NHPDLRPKSH PMDFEEYTDA FLRRYKDHFQ LDVPDNLTLQ GYLLGSKLGA KTYSYKRNTQ GQHDKRIHK RDLANVVRRH FDEHSIKETD CIPQFIYKVK NQ

UniProtKB: Transcriptional regulatory protein SAP30

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Macromolecule #6: Transcriptional regulatory protein RXT3

MacromoleculeName: Transcriptional regulatory protein RXT3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 23.933775 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LPNVSSQSVL AFTEKHYPNK LKNLGTLYYN RFKEGSFDED STSYSDRHSF PYNLYDNTLP PPFLPAIGIQ NINNIATLKI TYEDIQASF NNIESPRKRN NEIWGCDIYS DDSDPILVLR HCGFKIGAPS GGSFHKLRRT PVNVTNQDNV TGNLPLLEGT P FDLEVELL ...String:
LPNVSSQSVL AFTEKHYPNK LKNLGTLYYN RFKEGSFDED STSYSDRHSF PYNLYDNTLP PPFLPAIGIQ NINNIATLKI TYEDIQASF NNIESPRKRN NEIWGCDIYS DDSDPILVLR HCGFKIGAPS GGSFHKLRRT PVNVTNQDNV TGNLPLLEGT P FDLEVELL FLPTLQKYPS VKRFDITSRE WGSEATVIHD GLSYGIYSIV IKQ

UniProtKB: Transcriptional regulatory protein RXT3

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Macromolecule #7: Transcriptional regulatory protein PHO23

MacromoleculeName: Transcriptional regulatory protein PHO23 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 12.360187 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
LNDITDVLEE FPLATSRYLT LLHEIDAKCV HSMPNLNERI DKFLKKDFNK DHQTQVRLLN NINKIYEELM PSLEEKMHVS SIMLDNLDR LTSRLELAYE VAIKNT

UniProtKB: Transcriptional regulatory protein PHO23

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Macromolecule #8: Transcriptional regulatory protein RXT2

MacromoleculeName: Transcriptional regulatory protein RXT2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 24.683771 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SKLVNVKEIL TPILSLGDII NHKTISRTFS SPILKNLALQ IILMIEKEQM SVVRYSQFLE VFLGDHPEPI YESNLNLPSY NHNLTLPED RGASDEDDIN NKNNINEVNS NSLSTEAGHI NNGMEEFGEE DPFFALPRLE QSNALLSLLP SSSGSASIST L TAAEQQQL ...String:
SKLVNVKEIL TPILSLGDII NHKTISRTFS SPILKNLALQ IILMIEKEQM SVVRYSQFLE VFLGDHPEPI YESNLNLPSY NHNLTLPED RGASDEDDIN NKNNINEVNS NSLSTEAGHI NNGMEEFGEE DPFFALPRLE QSNALLSLLP SSSGSASIST L TAAEQQQL NEEIESARQL SQIALQRNKE FIRNLQKIRK SVIKANRIRG RILNWSREYL

UniProtKB: Transcriptional regulatory protein RXT2

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Macromolecule #9: Histone deacetylase complex subunit CTI6

MacromoleculeName: Histone deacetylase complex subunit CTI6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 28.742312 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TFMAREEKQY QRMLEKALKE SRRTSHQEDP ESYENDADIY QGDTDNHNGT TRLQTDVMLT EGKPDSVTND DMKESLRPSK EQSMEKTND VEKEASQEKE SSTGSAQDTE KTDEPILPLT SISSSEDDSR KASSRGSKRV SKPARKGNRT RRSNTSSDTN Q NRRSADIG ...String:
TFMAREEKQY QRMLEKALKE SRRTSHQEDP ESYENDADIY QGDTDNHNGT TRLQTDVMLT EGKPDSVTND DMKESLRPSK EQSMEKTND VEKEASQEKE SSTGSAQDTE KTDEPILPLT SISSSEDDSR KASSRGSKRV SKPARKGNRT RRSNTSSDTN Q NRRSADIG TDKPVKPRLP PQRTSLNEMR RRVSAILEFI SRTQWELSED QSDREEFVRF VENQHFVEKV DTIYNGYNES LS MMDDLTR EL

UniProtKB: Histone deacetylase complex subunit CTI6

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Macromolecule #10: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.722664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGR VTIAQGGVLP NIQSVLLP

UniProtKB: Histone H2A

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Macromolecule #11: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.406954 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTS

UniProtKB: Histone H2B

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Macromolecule #12: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.560538 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVALFED TNLCAIHAKR VTIMPKDIQ LARRIRGER

UniProtKB: Histone H3

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Macromolecule #13: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 9.066641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGF

UniProtKB: Histone H4

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Macromolecule #14: DNA (155-MER)

MacromoleculeName: DNA (155-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.115652 KDa
SequenceString: (DT)(DC)(DT)(DA)(DG)(DA)(DA)(DC)(DA)(DG) (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) ...String:
(DT)(DC)(DT)(DA)(DG)(DA)(DA)(DC)(DA)(DG) (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)(DC)(DC)(DA)(DG) (DG)(DG)

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Macromolecule #15: DNA (155-MER)

MacromoleculeName: DNA (155-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.577309 KDa
SequenceString: (DC)(DC)(DC)(DT)(DG)(DG)(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) ...String:
(DC)(DC)(DC)(DT)(DG)(DG)(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)(DC)(DT)(DG)(DT)(DT)(DC)(DT)(DA) (DG)(DA)

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Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 1 / 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 KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8hpo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 451544
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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