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- EMDB-29892: Structure of the yeast (HDAC) Rpd3L complex -

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Basic information

Entry
Database: EMDB / ID: EMD-29892
TitleStructure of the yeast (HDAC) Rpd3L complex
Map data
Sample
  • Complex: Rpd3L
    • Protein or peptide: Transcriptional regulatory protein SDS3
    • Protein or peptide: Transcriptional regulatory protein SIN3
    • Protein or peptide: Transcriptional regulatory protein SAP30
    • Protein or peptide: Transcriptional regulatory protein PHO23
    • Protein or peptide: Transcriptional regulatory protein RXT2
    • Protein or peptide: Transcriptional regulatory protein DEP1
    • Protein or peptide: Histone deacetylase RPD3
    • Protein or peptide: Transcriptional regulatory protein RXT3
  • Ligand: ZINC ION
KeywordsHDAC / Silencing / chromatin / TRANSCRIPTION
Function / homology
Function and homology information


negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / positive regulation of inositol biosynthetic process / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / 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 / negative regulation of phosphatidylcholine biosynthetic process / positive regulation of inositol biosynthetic process / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex / negative regulation of reciprocal meiotic recombination / positive regulation of invasive growth in response to glucose limitation / negative regulation of silent mating-type cassette heterochromatin formation / invasive growth in response to glucose limitation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / SUMOylation of transcription cofactors / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / cell adhesion involved in single-species biofilm formation / histone deacetylase / SUMOylation of chromatin organization proteins / regulation of DNA-templated DNA replication initiation / cellular response to nitrogen starvation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone deacetylase complex / Ub-specific processing proteases / methylated histone binding / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / transcription coregulator activity / heterochromatin formation / histone deacetylase binding / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / transcription corepressor activity / G2/M transition of mitotic cell cycle / nucleosome assembly / chromatin organization / cellular response to heat / response to oxidative stress / transcription coactivator activity / 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 / mitochondrion / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
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
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 RXT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPatel AB / Radhakrishnan I / He Y
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144559 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01CA092584 United States
American Heart Association17GRNT33680167 United States
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.
Authors: Avinash B Patel / Jinkang Qing / Kelly H Tam / Sara Zaman / Maria Luiso / Ishwar Radhakrishnan / Yuan He /
Abstract: The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA- ...The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
History
DepositionFeb 22, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29892.png

Downloads & links

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Map

FileDownload / File: emd_29892.map.gz / Format: CCP4 / Size: 76.8 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.)
1.65 Å/pix.
x 272 pix.
= 449.344 Å		1.65 Å/pix.
x 272 pix.
= 449.344 Å		1.65 Å/pix.
x 272 pix.
= 449.344 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.040165387 - 0.07303285
Average (Standard dev.)0.000010551469 (±0.0014616768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 449.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29892_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_29892_half_map_1.map
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Half map: #1

Fileemd_29892_half_map_2.map
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Sample components

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Entire : Rpd3L

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

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Supramolecule #1: Rpd3L

SupramoleculeName: Rpd3L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Transcriptional regulatory protein SDS3

MacromoleculeName: Transcriptional regulatory protein SDS3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.685301 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 ISLIRELTGQ PPA PFRLRS D

UniProtKB: Transcriptional regulatory protein SDS3

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Macromolecule #2: Transcriptional regulatory protein SIN3

MacromoleculeName: Transcriptional regulatory protein SIN3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Transcriptional regulatory protein SIN3

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Macromolecule #3: Transcriptional regulatory protein SAP30

MacromoleculeName: Transcriptional regulatory protein SAP30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 23.064215 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 HFDEHSIKET DCIPQFIYKV KNQKKKFKME FRG

UniProtKB: Transcriptional regulatory protein SAP30

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Macromolecule #4: Transcriptional regulatory protein PHO23

MacromoleculeName: Transcriptional regulatory protein PHO23 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Transcriptional regulatory protein PHO23

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Macromolecule #5: Transcriptional regulatory protein RXT2

MacromoleculeName: Transcriptional regulatory protein RXT2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.684082 KDa
SequenceString: MTIRSSMKNN AELESKSVLA NESNIISTFT RRIIKEKSGN YQVLKRSLDG KLIYPEATGI SSNRGNKLLQ RSEVVTRRDL NNSKPMIEQ TVFYNGSEHR LLQTNIVTDS RRKRIKFTPD INVEPVLVGD ENDIDGSEKE DENITDEYYG EEDDDDLSKL V NVKEILTP ...String:
MTIRSSMKNN AELESKSVLA NESNIISTFT RRIIKEKSGN YQVLKRSLDG KLIYPEATGI SSNRGNKLLQ RSEVVTRRDL NNSKPMIEQ TVFYNGSEHR LLQTNIVTDS RRKRIKFTPD INVEPVLVGD ENDIDGSEKE DENITDEYYG EEDDDDLSKL V NVKEILTP ILSLGDIINH KTISRTFSSP ILKNLALQII LMIEKEQMSV VRYSQFLEVF LGDHPEPIYE SNLNLPSYNH NL TLPEDRG ASDEDDINNK NNINEVNSNS LSTEAGHINN GMEEFGEEDP FFALPRLEQS NALLSLLPSS SGSASISTLT AAE QQQLNE EIESARQLSQ IALQRNKEFI RNLQKIRKSV IKANRIRGRI LNWSREYLGI SDDDITIPVA LRVVKRGLIS ATTN KTTNF EEEIENTMED GVVDDNEPDE EANRA

UniProtKB: Transcriptional regulatory protein RXT2

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Macromolecule #6: Transcriptional regulatory protein DEP1

MacromoleculeName: Transcriptional regulatory protein DEP1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Transcriptional regulatory protein DEP1

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Macromolecule #7: Histone deacetylase RPD3

MacromoleculeName: Histone deacetylase RPD3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Histone deacetylase RPD3

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Macromolecule #8: Transcriptional regulatory protein RXT3

MacromoleculeName: Transcriptional regulatory protein RXT3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Transcriptional regulatory protein RXT3

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 2 / 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: 7.9
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 210993
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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