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- EMDB-35092: Cryo-EM structure of the SIN3S complex from S. pombe -

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Basic information

Entry
Database: EMDB / ID: EMD-35092
TitleCryo-EM structure of the SIN3S complex from S. pombe
Map data
Sample
  • Complex: The SIN3S complex
    • Protein or peptide: Cph1
    • Protein or peptide: Paired amphipathic helix protein pst2
    • Protein or peptide: Histone deacetylase clr6
    • Protein or peptide: RbAp48-related WD40 repeat-containing protein prw1
    • Protein or peptide: Chromatin modification-related protein eaf3
    • Protein or peptide: Uncharacterized protein C2F7.07c
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION
KeywordsSIN3 / SIN3S / Pst2 / Clr6 / deacetylase / DNA BINDING PROTEIN
Function / homology
Function and homology information


histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / HDACs deacetylate histones / histone H4K12 deacetylase activity, hydrolytic mechanism / SUMOylation of chromatin organization proteins / H3-H4 histone complex chaperone activity / histone H3K9 deacetylase activity, hydrolytic mechanism / Rpd3L complex ...histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / HDACs deacetylate histones / histone H4K12 deacetylase activity, hydrolytic mechanism / SUMOylation of chromatin organization proteins / H3-H4 histone complex chaperone activity / histone H3K9 deacetylase activity, hydrolytic mechanism / Rpd3L complex / Rpd3L-Expanded complex / Rpd3S complex / histone deacetylase / protein lysine deacetylase activity / histone deacetylase activity / DNA repair-dependent chromatin remodeling / Sin3-type complex / NuA4 histone acetyltransferase complex / transcription initiation-coupled chromatin remodeling / epigenetic regulation of gene expression / mitotic spindle / transcription corepressor activity / heterochromatin formation / histone binding / molecular adaptor activity / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm / cytosol
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-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / 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. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Paired amphipathic helix protein pst2 / Chromatin modification-related protein eaf3 / RbAp48-related WD40 repeat-containing protein prw1 / Histone deacetylase clr6 / Uncharacterized protein C2F7.07c / Uncharacterized protein C16C9.05
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang C / Guo Z / Zhan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2023
Title: Two assembly modes for SIN3 histone deacetylase complexes.
Authors: Chengcheng Wang / Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Xiechao Zhan /
Abstract: The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes ...The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes.
History
DepositionJan 10, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35092.png

Downloads & links

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Map

FileDownload / File: emd_35092.map.gz / Format: CCP4 / Size: 178 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.)
1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.7649817 - 7.4293528
Average (Standard dev.)-0.00095589133 (±0.102276616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35092_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35092_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : The SIN3S complex

EntireName: The SIN3S complex
Components
  • Complex: The SIN3S complex
    • Protein or peptide: Cph1
    • Protein or peptide: Paired amphipathic helix protein pst2
    • Protein or peptide: Histone deacetylase clr6
    • Protein or peptide: RbAp48-related WD40 repeat-containing protein prw1
    • Protein or peptide: Chromatin modification-related protein eaf3
    • Protein or peptide: Uncharacterized protein C2F7.07c
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: The SIN3S complex

SupramoleculeName: The SIN3S complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Macromolecule #1: Cph1

MacromoleculeName: Cph1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 45.046082 KDa
SequenceString: MASSINNSSQ PTVPSISNNS HGDSFVNEGP PSNFKNNSLT SSTHSSTDHV NVLPISQDKE MDISSPVKKQ KASYSNKSPN KAPIQKSRG SSLKSHLETE SQQTPVKRRR RKATIRNVDY CSACGGRGLF ICCEGCPCSF HLSCLEPPLT PENIPEGSWF C VTCSIKSH ...String:
MASSINNSSQ PTVPSISNNS HGDSFVNEGP PSNFKNNSLT SSTHSSTDHV NVLPISQDKE MDISSPVKKQ KASYSNKSPN KAPIQKSRG SSLKSHLETE SQQTPVKRRR RKATIRNVDY CSACGGRGLF ICCEGCPCSF HLSCLEPPLT PENIPEGSWF C VTCSIKSH HPPKHPLSIW SQLYDWIDSQ NPSQYRLPDD LVHYFHGISR GDTGAYKETE GEMDTDEFSA LPTGSSITNL AY CGYCSKP SMGACWVYGC QLCDTFYHKN CKEHAKKCSH DSIGKKGMRV PKNAVVIRTP LVLDTTSNTL NPKVMISGWQ FLM GEFPSD ELLYFPRLPV SCLYKVSEDG LIKDFLYAIG IEAKKFNNER KKRELEVIPP DVKSALLPAR THPNLPIALR TLFN KART

UniProtKB: Uncharacterized protein C16C9.05

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Macromolecule #2: Paired amphipathic helix protein pst2

MacromoleculeName: Paired amphipathic helix protein pst2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 125.011609 KDa
SequenceString: MEQTLAILKN DNSTLVAEMQ NQLVHDFSPN GTALPELDIK AFVQKLGQRL CHRPYVYSAF MDVVKALHNE IVDFPGFIER ISVILRDYP DLLEYLNIFL PSSYKYLLSN SGANFTLQFT TPSGPVSTPS TYVATYNDLP CTYHRAIGFV SRVRRALLSN P EQFFKLQD ...String:
MEQTLAILKN DNSTLVAEMQ NQLVHDFSPN GTALPELDIK AFVQKLGQRL CHRPYVYSAF MDVVKALHNE IVDFPGFIER ISVILRDYP DLLEYLNIFL PSSYKYLLSN SGANFTLQFT TPSGPVSTPS TYVATYNDLP CTYHRAIGFV SRVRRALLSN P EQFFKLQD SLRKFKNSEC SLSELQTIVT SLLAEHPSLA HEFHNFLPSS IFFGSKPPLG SFPLRGIQSS QFTLSNISDL LS QSRPDNL SPFSHLSNES SDFFKNVKNV LTDVETYHEF LKLLNLYVQG IIDRNILVSR GFGFLKSNSG LWRSFLSLTS LSP EEFLSV YNSACSDFPE CGPSYRLLPV EERNISCSGR DDFAWGILND DWVSHPTWAS EESGFIVQRK TPYEEAMTKL EEER YEFDR HIEATSWTIK SLKKIQNRIN ELPEEERETY TLEEGLGLPS KSIYKKTIKL VYTSEHAEEM FKALERMPCL TLPLV ISRL EEKNEEWKSV KRSLQPGWRS IEFKNYDKSL DSQCVYFKAR DKKNVSSKFL LAEADILRSQ AKLHFPLRSR SAFEFS FVY DNEIVLFDTC YMVCTYIVCN SPSGLKKVEH FFKNILPLHF GLEKDKFSIF LDQVFRGPDY DVNAPNIVGN KPVRRKR SN SITQLTEFVK QPKINGQRES RSAAAARKKE ESGNKSQSNS QNSLSDESGN VTPVSKKQLS QPAAAIKASL KYPSHPDS L LEHQDHAGDT ENEMHDDVDK EQFGYSSMYV FFRLFNLLYE RLYELQRLED QVSIIQQRII PNPVSQKQKI WRDRWNDLS DVPDEKTHYE NTYVMILRLI YGIVDQSAFE DYLRFYYGNK AYKIYTIDKL VWSAAKQVHH IVSDGKYKFV TSLVEQNSSA SPKKNYDDF LYRLEIEKLL NPDEILFRFC WINKFKSFGI KIMKRANLIV DQSLDTQRRV WKKYVQNYRI QKLTEEISYK N YRCPFLCR NIEKERTVEQ LVSRLQTKLL RSAELVSGLQ AKLCLDSFKL LYLPRTEDSY IDASYLRLRD TDFLDCQNKR KQ RWRNRWE SLLKSVRGTS DNTAEVNFDA DINALFIP

UniProtKB: Paired amphipathic helix protein pst2

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Macromolecule #3: Histone deacetylase clr6

MacromoleculeName: Histone deacetylase clr6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 46.165844 KDa
SequenceString: MGFGKKKVSY FYDEDVGNYH YGPQHPMKPH RVRMVHNLVV NYNLYEKLNV ITPVRATRND MTRCHTDEYI EFLWRVTPDT MEKFQPHQL KFNVGDDCPV FDGLYEFCSI SAGGSIGAAQ ELNSGNAEIA INWAGGLHHA KKREASGFCY VNDIALAALE L LKYHQRVL ...String:
MGFGKKKVSY FYDEDVGNYH YGPQHPMKPH RVRMVHNLVV NYNLYEKLNV ITPVRATRND MTRCHTDEYI EFLWRVTPDT MEKFQPHQL KFNVGDDCPV FDGLYEFCSI SAGGSIGAAQ ELNSGNAEIA INWAGGLHHA KKREASGFCY VNDIALAALE L LKYHQRVL YIDIDVHHGD GVEEFFYTTD RVMTCSFHKF GEYFPGTGHI KDTGIGTGKN YAVNVPLRDG IDDESYESVF KP VISHIMQ WFRPEAVILQ CGTDSLAGDR LGCFNLSMKG HSMCVDFVKS FNLPMICVGG GGYTVRNVAR VWTYETGLLA GEE LDENLP YNDYLQYYGP DYKLNVLSNN MENHNTRQYL DSITSEIIEN LRNLSFAPSV QMHKTPGDFT FENAEKQNIA KEEI MDERV

UniProtKB: Histone deacetylase clr6

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Macromolecule #4: RbAp48-related WD40 repeat-containing protein prw1

MacromoleculeName: RbAp48-related WD40 repeat-containing protein prw1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 48.528926 KDa
SequenceString: MAVSAVPHPS KQAQASEEGI NQEKCINEEY KIWKKNSPFL YDLIITRALE WPCMSLQWYP EQQIFAEHGY TEQKMFLGVR ADVGKYLLA VASIQLPYLN QTVPPTTMEG ASAGDESSLR VNISNLYSHP ESVCSAKLMP QDDSCVATVG NYHNDVLVFD K ESFESYSS ...String:
MAVSAVPHPS KQAQASEEGI NQEKCINEEY KIWKKNSPFL YDLIITRALE WPCMSLQWYP EQQIFAEHGY TEQKMFLGVR ADVGKYLLA VASIQLPYLN QTVPPTTMEG ASAGDESSLR VNISNLYSHP ESVCSAKLMP QDDSCVATVG NYHNDVLVFD K ESFESYSS ASESPLKPKY RLTKHTQPCT SVCWNFLSKG TLVSGSQDAT LSCWDLNAYN ESDSASVLKV HISSHEKQVS DV RFHYKHQ DLLASVSYDQ YLHVHDIRRP DASTKPARSV HAHSGPIHSV AFNPHNDFIL ATCSTDKTIA LWDLRNLNQR LHT LEGHED IVTKISFSPH EEPILASTSA DRRTLVWDLS RIGEDQPAEE AQDGPPELLF MHGGHTSCTI DMDWCPNYNW TMAT AAEDN ILQIWTPSRS IWGNEQLEED ATAYLS

UniProtKB: RbAp48-related WD40 repeat-containing protein prw1

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Macromolecule #5: Chromatin modification-related protein eaf3

MacromoleculeName: Chromatin modification-related protein eaf3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 39.191199 KDa
SequenceString: MAVSYKVNER VLCFHGPLLY EAKIVDTEMK GDVTTYLIHY KGWKNSWDEW VEQDRILQWT EENLKTQKEL KNAAISTRQK PTSKKSASS TSKHDSTGVK TSGKRSRESS TVTVDGDSHE LPSRIKTQKS ESPIPQQVKR DGTTDAKNEE TTKPENNEKD D FEEEPPLP ...String:
MAVSYKVNER VLCFHGPLLY EAKIVDTEMK GDVTTYLIHY KGWKNSWDEW VEQDRILQWT EENLKTQKEL KNAAISTRQK PTSKKSASS TSKHDSTGVK TSGKRSRESS TVTVDGDSHE LPSRIKTQKS ESPIPQQVKR DGTTDAKNEE TTKPENNEKD D FEEEPPLP KHKISVPDVL KLWLVDDWEN ITKNQQLIAI PRNPTVRAAI AAFRESKISH LNNEIDVDVF EQAMAGLVIY FN KCLGNML LYRFERQQYL EIRQQYPDTE MCDLYGVEHL IRLFVSLPEL IDRTNMDSQS IECLLNYIEE FLKYLVLHKD EYF IKEYQN APPNYRSLVG V

UniProtKB: Chromatin modification-related protein eaf3

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Macromolecule #6: Uncharacterized protein C2F7.07c

MacromoleculeName: Uncharacterized protein C2F7.07c / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 68.871703 KDa
SequenceString: MDAKPWNHTS EAFQASILED LKIIQKAGAE RNAKSSHGSI NSRSASPNKA TSRRNRAQNG NSNGRASVDN SDDGSKDDLD YSPSVKRKH VNGEGAEKGD HDTSNNGPSI TKLRRKVRRT YDTKDGFVAW NTLDDDFRPI VPDQERSRKI NPQKGNNNNL L KENKSLKT ...String:
MDAKPWNHTS EAFQASILED LKIIQKAGAE RNAKSSHGSI NSRSASPNKA TSRRNRAQNG NSNGRASVDN SDDGSKDDLD YSPSVKRKH VNGEGAEKGD HDTSNNGPSI TKLRRKVRRT YDTKDGFVAW NTLDDDFRPI VPDQERSRKI NPQKGNNNNL L KENKSLKT TAKDLSDISS SSMKKANNSS KPLFSGKLTF KANIPVPTSE VVTENNVTRN VTVYSNQKHL GNESENFNDM EG RAEDISS NELLPTPEEY PYRYNNDYCS ACHGPGNFLC CETCPNSFHF TCIDPPIEEK NLPDDAWYCN ECKHHSLYNE LDE QEELES NVKEEGTMVD VWMQLCTYID SHNPIQFHLP HSISSFFRGV GSGVMGEYIE TDVLKHLKSS RRSNGEERDP LLLK SKSGT PILCFRCHKS ALVSQSILAC DYCNSYWHPD CLNPPLATLP SNLRKWKCPN HSDHVTPRYR LPEKAKVIRV GLPRG FKNK GNIVIDENED EPSVQTIQLQ GKIRVVPSKP FKLNFLEQIR DNVINLRKMV EQDEQLCIET FSKFDFYATR DCELPL RIL CDVANDNLEN DDYVLALRDL LRISKWDPNQ PVPAPFDLAN LLSY

UniProtKB: Uncharacterized protein C2F7.07c

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 8 / Number of copies: 2 / 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

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 777199
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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