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- EMDB-37126: Rpd3S in complex with nucleosome with H3K36MLA modification and 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-37126
TitleRpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
Map data
Sample
  • Complex: H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3
    • Complex: Rpd3-Sin3-Eaf3-Rco1
      • Protein or peptide: x 4 types
    • Complex: histone
      • Protein or peptide: x 4 types
    • Complex: DNA
      • DNA: x 2 types
  • Ligand: x 1 types
KeywordsRpd3S / HDAC / Hho1 / cryptic transcription / TRANSCRIPTION
Function / homology
Function and homology information


nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3S complex / HDACs deacetylate histones / Rpd3L-Expanded complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3S complex / HDACs deacetylate histones / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / regulation of RNA stability / rDNA chromatin condensation / nucleophagy / SUMOylation of chromatin organization proteins / DNA replication-dependent chromatin assembly / nucleosome disassembly / histone deacetylase / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / positive regulation of macroautophagy / histone deacetylase complex / histone acetyltransferase complex / nuclear periphery / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / transcription corepressor activity / nucleosome / response to oxidative stress / transcription coactivator activity / cell cycle / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / 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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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 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. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Histone deacetylase / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Histone H4 / Transcriptional regulatory protein RCO1 / Chromatin modification-related protein EAF3 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsDong S / Li H / Wang M / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C ...Dong S / Li H / Wang M / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C / Zhou N / Shi X / Li M / Zhou M / Huang J / Zhang Y / Wong KH / Zhang X / Chao WCH / He J
Funding support China, 8 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC U20A2013 China
National Natural Science Foundation of China (NSFC)32241021 China
National Natural Science Foundation of China (NSFC)32170189 China
Other governmentMYRG2018-00221-FHS
Other government0009/2018/A1
Other government0032/2021/A1
Other government202102080156
Other government2019QN01Y051
CitationJournal: Cell Res / Year: 2023
Title: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang ...Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang / He Li / Ying Zhang / Koon Ho Wong / Xiaofei Zhang / William Chong Hang Chao / Jun He /
Abstract: In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA ...In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.
History
DepositionAug 9, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37126.png

Downloads & links

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Map

FileDownload / File: emd_37126.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.71 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.048621614 - 0.5426111
Average (Standard dev.)0.0017930422 (±0.010147836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 383.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37126_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_37126_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_37126_half_map_2.map
Projections & Slices
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Sample components

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Entire : H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3

EntireName: H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3
Components
  • Complex: H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3
    • Complex: Rpd3-Sin3-Eaf3-Rco1
      • Protein or peptide: Chromatin modification-related protein EAF3
      • Protein or peptide: Histone deacetylase RPD3
      • Protein or peptide: Transcriptional regulatory protein SIN3
      • Protein or peptide: Transcriptional regulatory protein RCO1
    • Complex: histone
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: 187bp DNA
      • DNA: 187bp DNA
  • Ligand: ZINC ION

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Supramolecule #1: H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3

SupramoleculeName: H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10

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Supramolecule #2: Rpd3-Sin3-Eaf3-Rco1

SupramoleculeName: Rpd3-Sin3-Eaf3-Rco1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #8-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: histone

SupramoleculeName: histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7

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Macromolecule #1: Chromatin modification-related protein EAF3

MacromoleculeName: Chromatin modification-related protein EAF3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.266406 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVDLEQEFAL GGRCLAFHGP LMYEAKILKI WDPSSKMYTS IPNDKPGGSS QATKEIKPQK LGEDESIPEE IINGKCFFIH YQGWKSSWD EWVGYDRIRA YNEENIAMKK RLANEAKEAK KSLLEQQKKK KLSTSLGGPS NGGKRKGDSR SNASISKSTS Q SFLTSSVS ...String:
MVDLEQEFAL GGRCLAFHGP LMYEAKILKI WDPSSKMYTS IPNDKPGGSS QATKEIKPQK LGEDESIPEE IINGKCFFIH YQGWKSSWD EWVGYDRIRA YNEENIAMKK RLANEAKEAK KSLLEQQKKK KLSTSLGGPS NGGKRKGDSR SNASISKSTS Q SFLTSSVS GRKSGRSSAN SLHPGSSLRS SSDQNGNDDR RRSSSLSPNM LHHIAGYPTP KISLQIPIKL KSVLVDDWEY VT KDKKICR LPADVTVEMV LNKYEHEVSQ ELESPGSQSQ LSEYCAGLKL YFDKCLGNML LYRLERLQYD ELLKKSSKDQ KPL VPIRIY GAIHLLRLIS VLPELISSTT MDLQSCQLLI KQTEDFLVWL LMHVDEYFND KDPNRSDDAL YVNTSSQYEG VALG M

UniProtKB: Chromatin modification-related protein EAF3

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Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.313943 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGV(M3L)KPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEASEAY LVALFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #8: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.961957 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHAKKSEASG F CYLNDIVL ...String:
MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHAKKSEASG F CYLNDIVL GIIELLRYHP RVLYIDIDVH HGDGVEEAFY TTDRVMTCSF HKYGEFFPGT GELRDIGVGA GKNYAVNVPL RD GIDDATY RSVFEPVIKK IMEWYQPSAV VLQCGGDSLS GDRLGCFNLS MEGHANCVNY VKSFGIPMMV VGGGGYTMRN VAR TWCFET GLLNNVVLDK DLPYNEYYEY YGPDYKLSVR PSNMFNVNTP EYLDKVMTNI FANLENTKYA PSVQLNHTPR DAED LGDVE EDSAEAKDTK GGSQYARDLH VEHDNEFY

UniProtKB: Histone deacetylase RPD3

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Macromolecule #9: Transcriptional regulatory protein SIN3

MacromoleculeName: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 157.586844 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHP QLAMWSHPQF EKGGGSGGGS GGGSWSHPQF EKENLYFQSD YRPLNVKDAL SYLEQVKFQF SSRPDIYNLF LDIMKDFKS QAIDTPGVIE RVSTLFRGYP ILIQGFNTFL PQGYRIECSS NPDDPIRVTT PMGTTTVNNN ISPSGRGTTD A QELGSFPE ...String:
MHHHHHHHHP QLAMWSHPQF EKGGGSGGGS GGGSWSHPQF EKENLYFQSD YRPLNVKDAL SYLEQVKFQF SSRPDIYNLF LDIMKDFKS QAIDTPGVIE RVSTLFRGYP ILIQGFNTFL PQGYRIECSS NPDDPIRVTT PMGTTTVNNN ISPSGRGTTD A QELGSFPE SDGNGVQQPS NVPMVPSSVY QSEQNQDQQQ SLPLLATSSG LPSIQQPEMP AHRQIPQSQS LVPQEDAKKN VD VEFSQAI SYVNKIKTRF ADQPDIYKHF LEILQTYQRE QKPINEVYAQ VTHLFQNAPD LLEDFKKFLP DSSASANQQV QHA QQHAQQ QHEAQMHAQA QAQAQAQAQV EQQKQQQQFL YPASGYYGHP SNRGIPQQNL PPIGSFSPPT NGSTVHEAYQ DQQH MQPPH FMPLPSIVQH GPNMVHQGIA NENPPLSDLR TSLTEQYAPS SIQHQQQHPQ SISPIANTQY GDIPVRPEID LDPSI VPVV PEPTEPIENN ISLNEEVTFF EKAKRYIGNK HLYTEFLKIL NLYSQDILDL DDLVEKVDFY LGSNKELFTW FKNFVG YQE KTKCIENIVH EKHRLDLDLC EAFGPSYKRL PKSDTFMPCS GRDDMCWEVL NDEWVGHPVW ASEDSGFIAH RKNQYEE TL FKIEEERHEY DFYIESNLRT IQCLETIVNK IENMTENEKA NFKLPPGLGH TSMTIYKKVI RKVYDKERGF EIIDALHE H PAVTAPVVLK RLKQKDEEWR RAQREWNKVW RELEQKVFFK SLDHLGLTFK QADKKLLTTK QLISEISSIK VDQTNKKIH WLTPKPKSQL DFDFPDKNIF YDILCLADTF ITHTTAYSNP DKERLKDLLK YFISLFFSIS FEKIEESLYS HKQNVSESSG SDDGSSIAS RKRPYQQEMS LLDILHRSRY QKLKRSNDED GKVPQLSEPP EEEPNTIEEE ELIDEEAKNP WLTGNLVEEA N SQGIIQNR SIFNLFANTN IYIFFRHWTT IYERLLEIKQ MNERVTKEIN TRSTVTFAKD LDLLSSQLSE MGLDFVGEDA YK QVLRLSR RLINGDLEHQ WFEESLRQAY NNKAFKLYTI DKVTQSLVKH AHTLMTDAKT AEIMALFVKD RNASTTSAKD QII YRLQVR SHMSNTENMF RIEFDKRTLH VSIQYIALDD LTLKEPKADE DKWKYYVTSY ALPHPTEGIP HEKLKIPFLE RLIE FGQDI DGTEVDEEFS PEGISVSTLK IKIQPITYQL HIENGSYDVF TRKATNKYPT IANDNTQKGM VSQKKELISK FLDCA VGLR NNLDEAQKLS MQKKWENLKD SIAKTSAGNQ GIESETEKGK ITKQEQSDNL DSSTASVLPA SITTVPQDDN IETTGN TES SDKGAKIQ

UniProtKB: Transcriptional regulatory protein SIN3

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Macromolecule #10: Transcriptional regulatory protein RCO1

MacromoleculeName: Transcriptional regulatory protein RCO1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.469328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE RSFKNEHSNL AVEDNIPEEE PKELLEKDS KGNIIKLNEP STISEDSKVS VTGLPLNKGP SEKIKRESLW NYRKNLGGQS NNSEMTLVPS KRFTQVPKNF Q DLNRNDLK ...String:
MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE RSFKNEHSNL AVEDNIPEEE PKELLEKDS KGNIIKLNEP STISEDSKVS VTGLPLNKGP SEKIKRESLW NYRKNLGGQS NNSEMTLVPS KRFTQVPKNF Q DLNRNDLK TFLTENMTEE SNIRSTIGWN GDIINRTRDR EPESDRDNKK LSNIRTKIIL STNATYDSKS KLFGQNSIKS TS NASEKIF RDKNNSTIDF ENEDFCSACN QSGSFLCCDT CPKSFHFLCL DPPIDPNNLP KGDWHCNECK FKIFINNSMA TLK KIESNF IKQNNNVKIF AKLLFNIDSH NPKQFQLPNY IKETFPAVKT GSRGQYSDEN DKIPLTDRQL FNTSYGQSIT KLDS YNPDT HIDSNSGKFL ICYKCNQTRL GSWSHPENSR LIMTCDYCQT PWHLDCVPRA SFKNLGSKWK CPLHSPTKVY KKIHH CQED NSVNYKVWKK QRLINKKNQL YYEPLQKIGY QNNGNIQIIP TTSHTDYDFN QDFKITQIDE NSIKYDFFDK IYKSKM VQK RKLFQFQESL IDKLVSNGSQ NGNSEDNMVK DIASLIYFQV SNNDKSSNNK SASKSNNLRK LWDLKELTNV VVPNELD SI QFNDFSSDEI KHLLYLKKII ESKPKEELLK FLNIENPENQ SEMHHHHHHH HPQLAMWSHP QFEKGGGSGG GSGGGSWS H PQFEKENLYF QS

UniProtKB: Transcriptional regulatory protein RCO1

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Macromolecule #6: 187bp DNA

MacromoleculeName: 187bp DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 58.077926 KDa
SequenceString: (DG)(DC)(DG)(DG)(DT)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(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) ...String:
(DG)(DC)(DG)(DG)(DT)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(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)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT) (DA) (DG)(DG)(DG)(DT)(DC)(DC)

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Macromolecule #7: 187bp DNA

MacromoleculeName: 187bp DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.397496 KDa
SequenceString: (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(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) ...String:
(DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(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)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC) (DC)(DA)(DC)(DC)(DG)(DC)

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / 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 state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68388
FSC plot (resolution estimation)

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