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- EMDB-34935: Cryo-EM structure of a SIN3/HDAC complex from budding yeast -

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Basic information

Entry
Database: EMDB / ID: EMD-34935
TitleCryo-EM structure of a SIN3/HDAC complex from budding yeast
Map data
Sample
  • Complex: The Rpd3L complex
    • Protein or peptide: x 10 types
  • Ligand: x 3 types
Function / homology
Function and homology information


: / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / : / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / positive regulation of invasive growth in response to glucose limitation / invasive growth in response to glucose limitation ...: / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / : / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / positive regulation of invasive growth in response to glucose limitation / invasive growth in response to glucose limitation / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / regulation of meiotic nuclear division / SUMOylation of transcription cofactors / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / NuRD complex / cell adhesion involved in single-species biofilm formation / histone deacetylase / SUMOylation of chromatin organization proteins / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / Ub-specific processing proteases / heterochromatin formation / histone acetyltransferase activity / methylated histone binding / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / transcription coregulator activity / histone deacetylase binding / double-strand break repair via nonhomologous end joining / transcription corepressor activity / nucleosome assembly / chromatin organization / histone binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell cycle / cell division / 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 / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / 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 ...Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / 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 / 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 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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 / Transcriptional regulatory protein UME1 / Transcriptional regulatory protein RXT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGuo Z / Zhan X / Wang C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of a SIN3-HDAC complex from budding yeast.
Authors: Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Yihang Xiao / Mingxuan Wu / Shuaixin Gao / Catherine C L Wong / Xiechao Zhan / Chengcheng Wang /
Abstract: SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM ...SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.
History
DepositionDec 12, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34935.png

Downloads & links

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Map

FileDownload / File: emd_34935.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.6639845 - 4.4420238
Average (Standard dev.)0.00095071626 (±0.066302985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 434.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34935_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34935_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The Rpd3L complex

EntireName: The Rpd3L complex
Components
  • Complex: The Rpd3L complex
    • Protein or peptide: Transcriptional regulatory protein UME1
    • Protein or peptide: Transcriptional regulatory protein SDS3
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: Transcriptional regulatory protein SAP30
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Transcriptional regulatory protein DEP1
    • Protein or peptide: Transcriptional regulatory protein PHO23
    • Protein or peptide: Transcriptional regulatory protein RXT2
    • Protein or peptide: Transcriptional regulatory protein RXT3
  • Ligand: PHOSPHOTHREONINE
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: The Rpd3L complex

SupramoleculeName: The Rpd3L complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Transcriptional regulatory protein UME1

MacromoleculeName: Transcriptional regulatory protein UME1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 51.075602 KDa
SequenceString: MSTLDIAEDN KIKNEEFKIW KKSIPSLYQH ISSLKPIFGS GVDESPSTLR SIVFTNDSSC NKSKGVLSVP LLYSQGSEIF EVDCIVPLG LHYKKPESIS EPLVQPDYTM ESQKVEQTVL IPKWEFKGET IAKMIYVDNS EINVKVIALS TNGSLAWFRE G VKSPVYTM ...String:
MSTLDIAEDN KIKNEEFKIW KKSIPSLYQH ISSLKPIFGS GVDESPSTLR SIVFTNDSSC NKSKGVLSVP LLYSQGSEIF EVDCIVPLG LHYKKPESIS EPLVQPDYTM ESQKVEQTVL IPKWEFKGET IAKMIYVDNS EINVKVIALS TNGSLAWFRE G VKSPVYTM MEPSTSLSSA SSGNQNKPCV DFAISNDSKT LTVTKEKHLD NENATIKLID NSGKIGEVLR TIPVPGIKNI QE IKFLNNQ IFATCSDDGI IRFWGNEIGK KPLWILNDSL DGKTTCFAAS PFVDTLFMTG TSGGALKVWD IRAVIALGDA DAE LNINQG HNKVNELFKV HHFYSEQVSK IEFSSISPME VVTIGGLGNV YHWNFEPVFA IYNEIHEDFQ GIISDELEAE SMAF YHTEG CRREIGENNK VNTVAYHKYI EDLVATVDSD GLLTVYKPFT GKVLDGSREV GAAKS

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Macromolecule #2: Transcriptional regulatory protein SDS3

MacromoleculeName: Transcriptional regulatory protein SDS3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 37.765277 KDa
SequenceString: MAIQKVSNKD LSRKDKRRFN IESKVNKIYQ NFYSERDNQY KDRLTALQTD LTSLHQGDNG QYARQVRDLE EERDLELVRL RLFEEYRVS RSGIEFQEDI EKAKAEHEKL IKLCKERLYS SIEQKIKKLQ EERLLMDVAN VHSYAMNYSR PQYQKNTRSH T VSGWDSSS ...String:
MAIQKVSNKD LSRKDKRRFN IESKVNKIYQ NFYSERDNQY KDRLTALQTD LTSLHQGDNG QYARQVRDLE EERDLELVRL RLFEEYRVS RSGIEFQEDI EKAKAEHEKL IKLCKERLYS SIEQKIKKLQ EERLLMDVAN VHSYAMNYSR PQYQKNTRSH T VSGWDSSS NEYGRDTANE SATDTGAGND RRTLRRRNAS KDTRGNNNNQ DESDFQTGNG SGSNGHGSRQ GSQFPHFNNL TY KSGMNSD SDFLQGINEG TDLYAFLFGE KNPKDNANGN EKKKNRGAQR YSTKTAPPLQ SLKPDEVTED I(SEP)LIRELTG QPPAPFRLRS D

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Macromolecule #3: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 49.361848 KDa
SequenceString: MVYEA(TPO)PFDP I(TPO)VKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQ EMCQFHT DEYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHA KKSEAS ...String:
MVYEA(TPO)PFDP I(TPO)VKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQ EMCQFHT DEYIDFLSRV TPDNLEMFKR ESVKFNVGDD CPVFDGLYEY CSISGGGSME GAARLNRGKC DVAVNYAGGL HHA KKSEAS GFCYLNDIVL GIIELLRYHP RVLYIDIDVH HGDGVEEAFY TTDRVMTCSF HKYGEFFPGT GELRDIGVGA GKNY AVNVP LRDGIDDATY RSVFEPVIKK IMEWYQP(SEP)AV VLQCGGDSLS GDRLGCFNLS MEGHANCVNY VKSFGIPMMV V GGGGYTMR NVARTWCFET GLLNNVVLDK DLPYNEYYEY YGPDYKLSVR PSNMFNVN(TPO)P EYLDKVMTNI FANLENTK Y AP(SEP)VQLNHTP RDAEDLGDVE EDSAEAKDTK GGSQYARDLH VEHDNEFY

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Macromolecule #4: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 48.961957 KDa
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

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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: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 23.144193 KDa
SequenceString: MARPVNTNAE TESRGRPTQG GGYASNNNGS CNNNNGSNNN NNNNNNNNNN SNNSNNNNGP TSSGRTNGKQ RLTAAQQQYI KNLIETHIT DNHPDLRPKS HPMDFEEYTD AFLRRYKDHF QLDVPDNLTL QGYLLGSKLG AKTYSYKRNT QGQHDKRIHK R DLANVVRR ...String:
MARPVNTNAE TESRGRPTQG GGYASNNNGS CNNNNGSNNN NNNNNNNNNN SNNSNNNNGP TSSGRTNGKQ RLTAAQQQYI KNLIETHIT DNHPDLRPKS HPMDFEEYTD AFLRRYKDHF QLDVPDNLTL QGYLLGSKLG AKTYSYKRNT QGQHDKRIHK R DLANVVRR HFDEH(SEP)IKET DCIPQFIYKV KNQKKKFKME FRG

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Macromolecule #6: Transcriptional regulatory protein SIN3

MacromoleculeName: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 175.047266 KDa
SequenceString: MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE EDRRDSNGQQ ALTSHAAHIL GYPPPHSNA MPSIATDSAL KQPHEYHPRP KSSSSSPSIN ASLMNAGPAP LPTVGAASFS LSRFDNPLPI KAPVHTEEPK S YNGLQEEE ...String:
MSQVWHNSNS QSNDVATSND ATGSNERNEK EPSLQGNKPG FVQQQQRITL PSLSALSTKE EDRRDSNGQQ ALTSHAAHIL GYPPPHSNA MPSIATDSAL KQPHEYHPRP KSSSSSPSIN ASLMNAGPAP LPTVGAASFS LSRFDNPLPI KAPVHTEEPK S YNGLQEEE KATQRPQDCK EVPAGVQPAD APDPSSNHAD ANDDNNNNEN SHDEDADYRP LNVKDALSYL EQVKFQFSSR PD IYNLFLD IMKDFKSQAI DTPGVIERVS TLFRGYPILI QGFNTFLPQG YRIECSSNPD DPIRVTTPMG TTTVNNNISP SGR GTTDAQ ELGSFPESDG NGVQQPSNVP MVPSSVYQSE QNQDQQQSLP LLATSSGLPS IQQPEMPAHR QIPQSQSLVP QEDA KKNVD VEFSQAISYV NKIKTRFADQ PDIYKHFLEI LQTYQREQKP INEVYAQVTH LFQNAPDLLE DFKKFLPDSS ASANQ QVQH AQQHAQQQHE AQMHAQAQAQ AQAQAQVEQQ KQQQQFLYPA SGYYGHPSNR GIPQQNLPPI GSFSPPTNGS TVHEAY QDQ QHMQPPHFMP LPSIVQHGPN MVHQGIANEN PPLSDLRTSL TEQYAPSSIQ HQQQHPQSIS PIANTQYGDI PVRPEID LD PSIVPVVPEP TEPIENNISL NEEVTFFEKA KRYIGNKHLY TEFLKILNLY SQDILDLDDL VEKVDFYLGS NKELFTWF K NFVGYQEKTK CIENIVHEKH RLDLDLCEAF GPSYKRLPKS DTFMPCSGRD DMCWEVLNDE WVGHPVWASE DSGFIAHRK NQYEETLFKI EEERHEYDFY IESNLRTIQC LETIVNKIEN MTENEKANFK LPPGLGHTSM TIYKKVIRKV YDKERGFEII DALHEHPAV TAPVVLKRLK QKDEEWRRAQ REWNKVWREL EQKVFFKSLD HLGLTFKQAD KKLLTTKQLI SEISSIKVDQ T NKKIHWLT PKPKSQLDFD FPDKNIFYDI LCLADTFITH TTAYSNPDKE RLKDLLKYFI SLFFSISFEK IEESLYSHKQ NV SESSGSD DGSSIASRKR PYQQEMSLLD ILHRSRYQKL KRSNDEDGKV PQLSEPPEEE PNTIEEEELI DEEAKNPWLT GNL VEEANS QGIIQNRSIF NLFANTNIYI FFRHWTTIYE RLLEIKQMNE RVTKEINTRS TVTFAKDLDL LSSQLSEMGL DFVG EDAYK QVLRLSRRLI NGDLEHQWFE ESLRQAYNNK AFKLYTIDKV TQSLVKHAHT LMTDAKTAEI MALFVKDRNA STTSA KDQI IYRLQVRSHM SNTENMFRIE FDKRTLHVSI QYIALDDLTL KEPKADEDKW KYYVTSYALP HPTEGIPHEK LKIPFL ERL IEFGQDIDGT EVDEEFSPEG ISVSTLKIKI QPITYQLHIE NGSYDVFTRK ATNKYPTIAN DNTQKGMVSQ KKELISK FL DCAVGLRNNL DEAQKLSMQK KWENLKDSIA KTSAGNQGIE SETEKGKITK QEQSDNLDSS TASVLPASIT TVPQDDNI E TTGNTESSDK GAKIQ

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Macromolecule #7: Transcriptional regulatory protein DEP1

MacromoleculeName: Transcriptional regulatory protein DEP1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 47.035723 KDa
SequenceString: MSQQTPQESE QTTAKEQDLD QESVLSNIDF NTDLNHNLNL SEYCISSDAG TEKMDSDEEK SLANLPELKY APKLSSLVKQ ETLTESLKR PHEDEKEAID EAKKMKVPGE NEDESKEEEK SQELEEAIDS KEKSTDARDE QGDEGDNEEE NNEEDNENEN E HTAPPALV ...String:
MSQQTPQESE QTTAKEQDLD QESVLSNIDF NTDLNHNLNL SEYCISSDAG TEKMDSDEEK SLANLPELKY APKLSSLVKQ ETLTESLKR PHEDEKEAID EAKKMKVPGE NEDESKEEEK SQELEEAIDS KEKSTDARDE QGDEGDNEEE NNEEDNENEN E HTAPPALV MPSPIEMEEQ RMTALKEITD IEYKFAQLRQ KLYDNQLVRL QTELQMCLEG SHPELQVYYS KIAAIRDYKL HR AYQRQKY ELSCINTETI ATRTFIHQDF HKKVTDLRAR LLNRTTQTWY DINKERRDMD IVIPDVNYHV PIKLDNKTLS CIT GYASAA QLCYPGEPVA EDLACESIEY RYRANPVDKL EVIVDRMRLN NEISDLEGLR KYFHSFPGAP ELNPLRDSEI NDDF HQWAQ

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Macromolecule #8: Transcriptional regulatory protein PHO23

MacromoleculeName: Transcriptional regulatory protein PHO23 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 37.08143 KDa
SequenceString: MSSPANLFPG LNDITDVLEE FPLATSRYLT LLHEIDAKCV HSMPNLNERI DKFLKKDFNK DHQTQVRLLN NINKIYEELM PSLEEKMHV SSIMLDNLDR LTSRLELAYE VAIKNTEIPR GLRLGVDNHP AMHLHHELME KIESKSNSKS SQALKSESRR E AMAANRRQ ...String:
MSSPANLFPG LNDITDVLEE FPLATSRYLT LLHEIDAKCV HSMPNLNERI DKFLKKDFNK DHQTQVRLLN NINKIYEELM PSLEEKMHV SSIMLDNLDR LTSRLELAYE VAIKNTEIPR GLRLGVDNHP AMHLHHELME KIESKSNSKS SQALKSESRR E AMAANRRQ GEHYSASTHQ QDDSKNDANY GGSRHESQDH TGNNTNSRKR ANAANTNNAD PETKKRKRRV ATTAVSPSTI ST ATAVNNG RIGTSTASRG VSSVGNSNNS RISRPKTNDY GEPLYCYCNQ VAYGEMVGCD GADCELEWFH LPCIGLETLP KGK WYCDDC KKKL

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Macromolecule #9: Transcriptional regulatory protein RXT2

MacromoleculeName: Transcriptional regulatory protein RXT2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 48.844043 KDa
SequenceString: MTIRSSMKNN AELESKSVLA NESNIISTFT RRIIKEKSGN YQVLKRSLDG KLIYPEATGI SSNRGNKLLQ RSEVVTRRDL NNSKPMIEQ TVFYNGSEHR LLQTNIVTDS RRKRIKFTPD INVEPVLVGD ENDIDGSEKE DENITDEYYG EEDDDDLSKL V NVKEIL(TPO)P ...String:
MTIRSSMKNN AELESKSVLA NESNIISTFT RRIIKEKSGN YQVLKRSLDG KLIYPEATGI SSNRGNKLLQ RSEVVTRRDL NNSKPMIEQ TVFYNGSEHR LLQTNIVTDS RRKRIKFTPD INVEPVLVGD ENDIDGSEKE DENITDEYYG EEDDDDLSKL V NVKEIL(TPO)P IL(SEP)LGDIINH KTISRTFSSP ILKNLALQII LMIEKEQMSV VRYSQFLEVF LGDHPEPIYE SNLN LPSYN HNLTLPEDRG ASDEDDINNK NNINEVNSNS LSTEAGHINN GMEEFGEEDP FFALPRLEQS NALLSLLPSS SGSAS ISTL TAAEQQQLNE EIESARQLSQ IALQRNKEFI RNLQKIRKSV IKANRIRGRI LNWSREYLGI SDDDITIPVA LRVVKR GLI SATTNKTTNF EEEIENTMED GVVDDNEPDE EANRA

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Macromolecule #10: Transcriptional regulatory protein RXT3

MacromoleculeName: Transcriptional regulatory protein RXT3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 33.851535 KDa
SequenceString: MSVSEQDPNR AYRETQSQIY KLQETLLNSA RTKNKQEEGQ ESNTHSFPEQ YMHYQNGRNS AYDLPNVSSQ SVLAFTEKHY PNKLKNLGT LYYNRFKEGS FDEDSTSYSD RHSFPYNLYD NTLPPPFLPA IGIQNINNIA TLKITYEDIQ ASFNNIESPR K RNNEIWGC ...String:
MSVSEQDPNR AYRETQSQIY KLQETLLNSA RTKNKQEEGQ ESNTHSFPEQ YMHYQNGRNS AYDLPNVSSQ SVLAFTEKHY PNKLKNLGT LYYNRFKEGS FDEDSTSYSD RHSFPYNLYD NTLPPPFLPA IGIQNINNIA TLKITYEDIQ ASFNNIESPR K RNNEIWGC DIYSDDSDPI LVLRHCGFKI GAPSGGSFHK LRRTPVNVTN QDNVTGNLPL LEGTPFDLEV ELLFLPTLQK YP SVKRFDI TSREWGSEAT VIHDGLSYGI YSIVIKQRLD RDKPHEPNGY IKNLKWT

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Macromolecule #11: PHOSPHOTHREONINE

MacromoleculeName: PHOSPHOTHREONINE / type: ligand / ID: 11 / Number of copies: 1 / Formula: TPO
Molecular weightTheoretical: 199.099 Da
Chemical component information

ChemComp-TPO:
PHOSPHOTHREONINE

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #13: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 13 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.3000000000000003 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 665105
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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