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- EMDB-37125: Rpd3S in complex with nucleosome with H3K36MLA modification and 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-37125
TitleRpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
Map data
Sample
  • Complex: H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2
    • Complex: Rpd3-Sin3-Eaf3-Rco1
      • Protein or peptide: x 4 types
    • Complex: Histone
      • Protein or peptide: x 4 types
    • Complex: 187bp 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 silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / histone deacetylase / nucleosome disassembly / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / negative regulation of transcription by RNA polymerase I / regulation of DNA-templated DNA replication initiation / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / positive regulation of macroautophagy / Estrogen-dependent gene expression / histone deacetylase complex / histone acetyltransferase complex / methylated histone binding / nuclear periphery / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / heterochromatin formation / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / G2/M transition of mitotic cell cycle / nucleosome / nucleosome assembly / cellular response to heat / response to oxidative stress / transcription coactivator activity / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / 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 / metal ion binding / cytoplasm
Similarity search - Function
: / : / MSL3 chromodomain-like / 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 ...: / : / MSL3 chromodomain-like / 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. / 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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: 2.9 Å
AuthorsDong S / Li H / Meilin W / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C ...Dong S / Li H / Meilin W / 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_37125.png

Downloads & links

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Map

FileDownload / File: emd_37125.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 540 pix.
= 383.4 Å		0.71 Å/pix.
x 540 pix.
= 383.4 Å		0.71 Å/pix.
x 540 pix.
= 383.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.060660526 - 0.59335476
Average (Standard dev.)0.0019794193 (±0.011249824)
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_37125_msk_1.map
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Half map: #2

Fileemd_37125_half_map_1.map
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Half map: #1

Fileemd_37125_half_map_2.map
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Sample components

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Entire : H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2

EntireName: H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2
Components
  • Complex: H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2
    • 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: 187bp 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) class2

SupramoleculeName: H3/H4 deacetylation state of Rpd3S-NCP (187bp/MLA) class2
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: 187bp DNA

SupramoleculeName: 187bp DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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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: 176.152438 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHS QVWHNSNSQS NDVATSNDAT GSNERNEKEP SLQGNKPGFV QQQQRITLPS LSALSTKEED RRDSNGQQAL TSHAAHILG YPPPHSNAMP SIATDSALKQ PHEYHPRPKS SSSSPSINAS LMNAGPAPLP TVGAASFSLS RFDNPLPIKA P VHTEEPKS ...String:
MHHHHHHHHS QVWHNSNSQS NDVATSNDAT GSNERNEKEP SLQGNKPGFV QQQQRITLPS LSALSTKEED RRDSNGQQAL TSHAAHILG YPPPHSNAMP SIATDSALKQ PHEYHPRPKS SSSSPSINAS LMNAGPAPLP TVGAASFSLS RFDNPLPIKA P VHTEEPKS YNGLQEEEKA TQRPQDCKEV PAGVQPADAP DPSSNHADAN DDNNNNENSH DEDADYRPLN VKDALSYLEQ VK FQFSSRP DIYNLFLDIM KDFKSQAIDT PGVIERVSTL FRGYPILIQG FNTFLPQGYR IECSSNPDDP IRVTTPMGTT TVN NNISPS GRGTTDAQEL GSFPESDGNG VQQPSNVPMV PSSVYQSEQN QDQQQSLPLL ATSSGLPSIQ QPEMPAHRQI PQSQ SLVPQ EDAKKNVDVE FSQAISYVNK IKTRFADQPD IYKHFLEILQ TYQREQKPIN EVYAQVTHLF QNAPDLLEDF KKFLP DSSA SANQQVQHAQ QHAQQQHEAQ MHAQAQAQAQ AQAQVEQQKQ QQQFLYPASG YYGHPSNRGI PQQNLPPIGS FSPPTN GST VHEAYQDQQH MQPPHFMPLP SIVQHGPNMV HQGIANENPP LSDLRTSLTE QYAPSSIQHQ QQHPQSISPI ANTQYGD IP VRPEIDLDPS IVPVVPEPTE PIENNISLNE EVTFFEKAKR YIGNKHLYTE FLKILNLYSQ DILDLDDLVE KVDFYLGS N KELFTWFKNF VGYQEKTKCI ENIVHEKHRL DLDLCEAFGP SYKRLPKSDT FMPCSGRDDM CWEVLNDEWV GHPVWASED SGFIAHRKNQ YEETLFKIEE ERHEYDFYIE SNLRTIQCLE TIVNKIENMT ENEKANFKLP PGLGHTSMTI YKKVIRKVYD KERGFEIID ALHEHPAVTA PVVLKRLKQK DEEWRRAQRE WNKVWRELEQ KVFFKSLDHL GLTFKQADKK LLTTKQLISE I SSIKVDQT NKKIHWLTPK PKSQLDFDFP DKNIFYDILC LADTFITHTT AYSNPDKERL KDLLKYFISL FFSISFEKIE ES LYSHKQN VSESSGSDDG SSIASRKRPY QQEMSLLDIL HRSRYQKLKR SNDEDGKVPQ LSEPPEEEPN TIEEEELIDE EAK NPWLTG NLVEEANSQG IIQNRSIFNL FANTNIYIFF RHWTTIYERL LEIKQMNERV TKEINTRSTV TFAKDLDLLS SQLS EMGLD FVGEDAYKQV LRLSRRLING DLEHQWFEES LRQAYNNKAF KLYTIDKVTQ SLVKHAHTLM TDAKTAEIMA LFVKD RNAS TTSAKDQIIY RLQVRSHMSN TENMFRIEFD KRTLHVSIQY IALDDLTLKE PKADEDKWKY YVTSYALPHP TEGIPH EKL KIPFLERLIE FGQDIDGTEV DEEFSPEGIS VSTLKIKIQP ITYQLHIENG SYDVFTRKAT NKYPTIANDN TQKGMVS QK KELISKFLDC AVGLRNNLDE AQKLSMQKKW ENLKDSIAKT SAGNQGIESE TEKGKITKQE QSDNLDSSTA SVLPASIT T VPQDDNIETT GNTESSDKGA KIQ

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: 78.951305 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 SE

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
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: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109319
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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