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- EMDB-51867: Cryo-EM structure of the SEAC wing - EGOC -

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Basic information

Entry
Database: EMDB / ID: EMD-51867
TitleCryo-EM structure of the SEAC wing - EGOC
Map dataDeepEMhancer sharpened map
Sample
  • Complex: SEAC-EGOC supercomplex
    • Complex: SEA complex wing
      • Protein or peptide: x 4 types
    • Complex: EGO complex
      • Protein or peptide: x 5 types
  • Ligand: x 3 types
KeywordsGTPase activating protein / GTPase / nutrient-sensing / amino acid signaling / cell growth / SIGNALING PROTEIN
Function / homology
Function and homology information


MTOR signalling / GATOR1 complex / pseudohyphal growth / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole ...MTOR signalling / GATOR1 complex / pseudohyphal growth / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole / Seh1-associated complex / Amino acids regulate mTORC1 / proline transport / regulation of TORC1 signaling / phosphate ion transport / regulation of autophagosome assembly / TORC1 signaling / endocytic recycling / vacuolar acidification / fungal-type vacuole membrane / negative regulation of TOR signaling / cellular response to nitrogen starvation / vacuolar membrane / transcription by RNA polymerase III / regulation of receptor recycling / positive regulation of TOR signaling / subtelomeric heterochromatin formation / transcription by RNA polymerase I / negative regulation of TORC1 signaling / signaling adaptor activity / positive regulation of TORC1 signaling / positive regulation of autophagy / negative regulation of autophagy / GTPase activator activity / cellular response to amino acid starvation / cellular response to starvation / meiotic cell cycle / cellular response to amino acid stimulus / late endosome membrane / late endosome / protein transport / cellular response to oxidative stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / chromosome, telomeric region / positive regulation of MAPK cascade / intracellular signal transduction / membrane raft / response to xenobiotic stimulus / GTPase activity / chromatin / GTP binding / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / : / : / RING/Ubox like zinc-binding domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 ...YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / : / : / RING/Ubox like zinc-binding domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / : / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1, N-terminal domain / DEPDC5 protein C-terminal region / GATOR1 complex protein NPRL3, C-terminal HTH / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / RagA/B / RWD domain / RagC/D / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / RWD domain profile. / RWD / RWD domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / WD domain, G-beta repeat / Winged helix DNA-binding domain superfamily / 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 / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein SLM4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / GTP-binding protein GTR2 / GTP-binding protein GTR1 / Protein MEH1 / Maintenance of telomere capping protein 5 / Protein EGO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTafur L / Loewith R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)AdG TENDOEuropean Union
CitationJournal: To Be Published
Title: Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex
Authors: Tafur L / Bonadei L / Zheng Y / Loewith R
History
DepositionOct 21, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51867.png

Downloads & links

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Map

FileDownload / File: emd_51867.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 512 pix.
= 522.701 Å		1.02 Å/pix.
x 512 pix.
= 522.701 Å		1.02 Å/pix.
x 512 pix.
= 522.701 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0209 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0544
Minimum - Maximum-0.0017881716 - 2.2575703
Average (Standard dev.)0.0004429116 (±0.01604491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 522.7008 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_51867_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map with a wide mask

Fileemd_51867_additional_2.map
AnnotationDeepEMhancer sharpened map with a wide mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Npr2 Latch Class 2 (unsharpened map)

Fileemd_51867_additional_3.map
AnnotationNpr2 Latch Class 2 (unsharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Npr2 Latch Class 3 (unsharpened map)

Fileemd_51867_additional_4.map
AnnotationNpr2 Latch Class 3 (unsharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Npr2 Latch Class 1 (unsharpened map)

Fileemd_51867_additional_5.map
AnnotationNpr2 Latch Class 1 (unsharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51867_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51867_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SEAC-EGOC supercomplex

EntireName: SEAC-EGOC supercomplex
Components
  • Complex: SEAC-EGOC supercomplex
    • Complex: SEA complex wing
      • Protein or peptide: Maintenance of telomere capping protein 5
      • Protein or peptide: Nitrogen permease regulator 2
      • Protein or peptide: Nitrogen permease regulator 3
      • Protein or peptide: Vacuolar membrane-associated protein IML1
    • Complex: EGO complex
      • Protein or peptide: GTP-binding protein GTR1
      • Protein or peptide: GTP-binding protein GTR2
      • Protein or peptide: Protein MEH1
      • Protein or peptide: Protein EGO2
      • Protein or peptide: Protein SLM4
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: SEAC-EGOC supercomplex

SupramoleculeName: SEAC-EGOC supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: SEA complex wing

SupramoleculeName: SEA complex wing / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: EGO complex

SupramoleculeName: EGO complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3, #7-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Maintenance of telomere capping protein 5

MacromoleculeName: Maintenance of telomere capping protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 131.104062 KDa
SequenceString: MCSSINEGPY NSPTFGKSLS LKVDGGFNAV SINPSGRDIV LASRQGLYII DLDDPFTPPR WLHHITPWQV ADVQWSPHPA KPYWIVSTS NQKAIIWNLA KSSSNAIEFV LHGHSRAITD INFNPQHPDV LATCSVDTYV HAWDMRSPHR PFYSTSSWRS A ASQVKWNY ...String:
MCSSINEGPY NSPTFGKSLS LKVDGGFNAV SINPSGRDIV LASRQGLYII DLDDPFTPPR WLHHITPWQV ADVQWSPHPA KPYWIVSTS NQKAIIWNLA KSSSNAIEFV LHGHSRAITD INFNPQHPDV LATCSVDTYV HAWDMRSPHR PFYSTSSWRS A ASQVKWNY KDPNVLASSH GNDIFVWDLR KGSTPLCSLK GHVSSVNSID FNRFKYSEIM SSSNDGTVKF WDYSKSTTES KR TVTTNFP IWRGRYLPFG EGYCIMPMVG GNNAVYLINL CDDDDSEQNK KTKLQPIYAF KGHSDRVIDF LWRSRHTCDG DYD DREFQL VTWSKDCDLK LWPISDSIYG KVNFDRGKRL EEKLPDYDYC SYNKEPENRE NVQKNEFRRL RENFVTTSGL KKNK TNHIT WLSGIRMNSA TSQEDLFNET KIQNLGEEVS AIGHKFPKVV FEKISVSTRE LCLTLNGPWS EENPDDYIFL RISIN FPLN YPNKGDPPKF TIEENSNLTM SKRQEILSNL ATIGQKYTDS NLYCLEPCIR FVLGEKVSLE DIEEGQEPLL NFDIAD HID FEELSSLDSS YSDSQNPENL SSQSDIESYK EALVFPDTSN QGLDFGRNLA LDTTPVPNGC GSCWTATGEL FCFFANE KK PEKKQNAIIK LSQKEAGVEK HPFKIEPQVL YDKEVDSSVI TAADELKARP KRYVDTLGLG GGTNGDSRTY FDDETSSD D SFDSVADDWD DILRNDIIVR TKIPILRGNF KAFSSVHSES GKTVESTKKN KNLVISKNFS SLLSDRKELA LEYLFMDAT PEGFARNNAL VAEKFDLDEI SHCWQILSDM LIDQSDYDPY TTIWNNHPMG IKWFIKEAIV YFERQQNLQM LAMLCCVILS ARRKKIPAR YYGQELENME GTIVFNDNES QNTSFWKGSD AFSTRSRSST VTPNFYGNHL RGKNIHGGDN SSIRSDDHHA R LRTHNTLN GSSKFTEPAQ KQGSRAISSS PFHSRMPDIK VELLHDDIIE AYEQEDLLHL EVSDIPKFQT YIYQYSKLLF RW GLPLERV KILKVSTDFR SSYSSQGIPP NNNKKSPYNG VLTHWIENNE FGEEKFLARN CNYCDLRVTR SSFICGNCQH VLH SSCARI WWEIGDECPS GCGCNCPEMF DA

UniProtKB: Maintenance of telomere capping protein 5

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Macromolecule #2: GTP-binding protein GTR1

MacromoleculeName: GTP-binding protein GTR1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 35.892465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSNNRKKLL LMGRSGSGKS SMRSIIFSNY SAFDTRRLGA TIDVEHSHLR FLGNMTLNLW DCGGQDVFME NYFTKQKDHI FQMVQVLIH VFDVESTEVL KDIEIFAKAL KQLRKYSPDA KIFVLLHKMD LVQLDKREEL FQIMMKNLSE TSSEFGFPNL I GFPTSIWD ...String:
MSSNNRKKLL LMGRSGSGKS SMRSIIFSNY SAFDTRRLGA TIDVEHSHLR FLGNMTLNLW DCGGQDVFME NYFTKQKDHI FQMVQVLIH VFDVESTEVL KDIEIFAKAL KQLRKYSPDA KIFVLLHKMD LVQLDKREEL FQIMMKNLSE TSSEFGFPNL I GFPTSIWD ESLYKAWSQI VCSLIPNMSN HQSNLKKFKE IMNALEIILF ERTTFLVICS SNGENSNENH DSSDNNNVLL DP KRFEKIS NIMKNFKQSC TKLKSGFKTL ILNNNIYVSE LSSNMVCFIV LKDMNIPQEL VLENIKKAKE FFQ

UniProtKB: GTP-binding protein GTR1

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Macromolecule #3: GTP-binding protein GTR2

MacromoleculeName: GTP-binding protein GTR2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.633961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLEATDSKA MVLLMGVRRC GKSSICKVVF HNMQPLDTLY LESTSNPSLE HFSTLIDLAV MELPGQLNYF EPSYDSERLF KSVGALVYV IDSQDEYINA ITNLAMIIEY AYKVNPSINI EVLIHKVDGL SEDFKVDAQR DIMQRTGEEL LELGLDGVQV S FYLTSIFD ...String:
MSLEATDSKA MVLLMGVRRC GKSSICKVVF HNMQPLDTLY LESTSNPSLE HFSTLIDLAV MELPGQLNYF EPSYDSERLF KSVGALVYV IDSQDEYINA ITNLAMIIEY AYKVNPSINI EVLIHKVDGL SEDFKVDAQR DIMQRTGEEL LELGLDGVQV S FYLTSIFD HSIYEAFSRI VQKLIPELSF LENMLDNLIQ HSKIEKAFLF DVNSKIYVST DSNPVDIQMY EVCSEFIDVT ID LFDLYKA PVLRNSQKSS DKDNVINPRN ELQNVSQLAN GVIIYLRQMI RGLALVAIIR PNGTDMESCL TVADYNIDIF KKG LEDIWA NARASQAKNS IEDDV

UniProtKB: GTP-binding protein GTR2

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Macromolecule #4: Nitrogen permease regulator 2

MacromoleculeName: Nitrogen permease regulator 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 69.937547 KDa
SequenceString: MLSYFQGFVP IHTIFYSVFH PTEGSKIKYE FPPNNLKNHG INFNTFKNYI IPKPILCHKL ITFKYGTYRI VCYPVTINSP IYARNFFSF NFVFVFPYDC ETSPYEPAIT RLGKMFKVLE EQNQLLSKSE RDPVFFDLKV LENSTTTPST AGPSSTPNPS S NTTPTHPT ...String:
MLSYFQGFVP IHTIFYSVFH PTEGSKIKYE FPPNNLKNHG INFNTFKNYI IPKPILCHKL ITFKYGTYRI VCYPVTINSP IYARNFFSF NFVFVFPYDC ETSPYEPAIT RLGKMFKVLE EQNQLLSKSE RDPVFFDLKV LENSTTTPST AGPSSTPNPS S NTTPTHPT SEKDTKDMRS SRYSDLIKDL GLPQSAFSIQ DLLMRIFQDL NNYSECLIPI DEGNAVDIKI FPLLRPPTTC VS LEDVPLS SVNLKKIIDV NWDPTMMSIV PYIDGLNSIA KISKLSNSDP GLVIECIRHL IYYKCVTLSD IFQFSNIYAP SSL IRNFLT DPLMASDCQS YVTFPEVSKI SNLPLNKSLG SGDQDSPSFS VRRKSKSSSI PSNPDSRTTS FSSTSRVSQN SSLN SSFSS IYKDWRQSQT SCSSSNIHVI NNRNRFLPTR SCLFDLYRSL SQGQTLKTWY ESKYMILKEN NIDIRRFITF GLEKR IIYR CYSFPVMINA GSREPKEMTP IITKDLVNND KLLEKRNHNH LLSATGSRNT AQSGNLKPER PSKVSFEMQR VSSLAT GKS TMPKLSDEEE GILEESIRNA ETFDKICVLL SKPKLEVESY LNELGEFKVI NS

UniProtKB: Nitrogen permease regulator 2

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Macromolecule #5: Nitrogen permease regulator 3

MacromoleculeName: Nitrogen permease regulator 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 130.141094 KDa
SequenceString: MDECLPNSCL LGVHLVISTH SGPQIVYHYP PSNTAFLTNN PTKHQHLYGN HANLNKNTST NKEEKLFNSG STKTASQIAL NESAKSYNT AITPSMTNTN TNNVTLPPTR SHANTVGSQS SIPAATNGVG YRKTDIEDTS RTFQYQETES ETSSSGLSDS E LSTDYLDI ...String:
MDECLPNSCL LGVHLVISTH SGPQIVYHYP PSNTAFLTNN PTKHQHLYGN HANLNKNTST NKEEKLFNSG STKTASQIAL NESAKSYNT AITPSMTNTN TNNVTLPPTR SHANTVGSQS SIPAATNGVG YRKTDIEDTS RTFQYQETES ETSSSGLSDS E LSTDYLDI SSDSFSISSS LSSSSLSSSP SSSSSSSPPQ DGLSRTNSSF QSTDSMSPTS PQMIMENDSI SVAESYLDSG TN NKSRAAS KRSQNFFHKL STKKSTDSKT HSPVRKLKSK PSQSTKKGNK LLKNTSNETD GNAFTGSCSI SSKKSLSSTG EHN QELRNS SLNDTPGQSP HHYHHRYHHY HKNAATSQRN SHTQYDVEEE DMEVSAMLQD GKISMNEIFF EEENFQDINK ILEF DNDFV AEFCSPEREM CNTRFEFTVD NFCFLGLPIH VDSQGRWRKS KHKNKTRSKR SSSTTTNISR KKSIASKISS LSENT LKKV NSGEADTVYD SNIGHEASTD TPNLRINTDV SGNEFEREKE DLGKNMNMFH VCFVMNPHLI EYNKRIDDMY QFVVTR LSL LLRYVQSKTS YISSECHIIL KEKERVLKHS KTYQSIRGAG NKGKYLYQRI LAKSSLARAL TECVDKIQRN EIACLEI ND DKVISLQIPI QNEFEKMPNF KLQPVLRGSY LTSILNMKFL EKSSLRIESQ NRQNDQAQFS DTNNNIYRFG NNINSTGH C GAANVDDGDD NESNYYCDDN DDLLNYALLL LDEPNNIISS LETFSYQDDI GTIILKHLVR NIQPNIPLRS YRYLITDLL DNPSSLDDLT TETNSLESSI LRSCALHLMY WRHARIVIPL SSKYTYIVSP LAPIQGYTID DYKSTSQNDG NVKKMDDREN NKSGSDRVP LIYQNSMLFR SKFPSLPSLP IFLSLLSTDK PQAYSNIIPS REHKPVYLNA LAWLIQYGYV TQLLTFINIR V DKHIKMAV DEDLEKEGFR KTNTARRPSM DYKKTDKKLD DEDGQSRDAN ASEACSGKNE GMQSNDNNKD VDEKDNENDS RV DDRDDNE IAIADEEEIL HFEYDDPEMQ HDYTIILEPE RATAIEKRWL YRCIYGQPSD IQILFNKLLK YFNGKVPMEL VII KEEISR HDLKKLLNAL DKYLIEIHHW

UniProtKB: Nitrogen permease regulator 3

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Macromolecule #6: Vacuolar membrane-associated protein IML1

MacromoleculeName: Vacuolar membrane-associated protein IML1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 182.203359 KDa
SequenceString: MFAKLHGKKQ RPISSINSQT PRTSNTTHAN SISLSSGNLI VGSNRNLRQK KEQFGSQQRA SGRKLISNKE NDDNVNNGGD NNYDNGERV HRHHIPGLKI KAYQAELGYH ESRFSENLVM LNLVEFPDIK PGDLVELKTY HKNPSASNGD KKIYFIAKDF D GETKRRAK ...String:
MFAKLHGKKQ RPISSINSQT PRTSNTTHAN SISLSSGNLI VGSNRNLRQK KEQFGSQQRA SGRKLISNKE NDDNVNNGGD NNYDNGERV HRHHIPGLKI KAYQAELGYH ESRFSENLVM LNLVEFPDIK PGDLVELKTY HKNPSASNGD KKIYFIAKDF D GETKRRAK TSNVSILSGQ LQTLLDLPSR SRIWIKLKPN KFDLQADVVE FNIKDCLLNR GDMWVLSSKL VDTCVFMDQR LA FLDSIRG TIKGIYRNGK KIVSGYIGEQ TRIIFRSESA RLIFLIQITD EMWNFEETGE QLFQKMVNSF FPKIFKKWKD VDT HHTITI AFAISMDLSD TSFKDLTPGE SLKNSQDYFR IVVDQVSIIH WVDIMETLRE EFMEIRKDLL NKQTDKGYSV ANGR FSPVI KSNFLELVNF ATTILTDPFK QLDLRHTTTH VMIISPGSGL FDVDYSLLRL TGKKLLSLEM TMDLICLSKA PLHIV PLFR YRDFENKLHH CVPLWLSVFF WNDHDKKSNS EWTPRCKIYD LQMMGITENE LIREVDVEYL QLNKKVKSLS EFMNDY DKN AFEVKILCAG SNTKQSKKLN SKFDTVFEND VVVKARKIPA TATTTHGNTK FIWRGPKVAL PAIKDIQKPN VIPDLSI KT IEASFYDDCN TTNDKISTPT TSNNDNLEMN DSLVSVRSAD NQNTSLALDS LKGLSKRNSL KDFTQRVITK FISNIDTS K NKKIKSTLLR DDVDNSPLGS NTPLPSSESK ISGLKLQQKG LADENVISKR GNLIIKKNLS IFGLPSNEIM SGSPSSYLG SSHTRTSSKL SNMSDKAAFI TEGQKSKHDD SNTYSLTQQL KHRISETWVD IKSPSIPVSS EFANELLPIR WKDVWPKYVA RKYSKWRSF TTPAELPITI SDFPSKDDFD RNFIFRNHSV TLNTDQEQYN QTYKDLLRDM IYMRLLTGFQ ICVGRQVEKI E LSRESGES ETVVNKYLDF NQNDAFKLYL MIDSEIHRIT CSSSGIIDVE RYLRKDEANL FDQVPSYIPL VKTRYESSFR DA MIDPLHV KRESLNWNQI DQVLAGYGDN LIDRKWHGFR AKYVVLPTDI PPNTYSMVIN GKSETLNPEE IRVEGLRRLI GSI TRSRLR TEKEKKGRKT KREEIQPEVM FYTGPLYNFI NEQQTSLESS AINFKDSIFV NDNNLLNRNV ELSKLAYQIQ RGED RITLV NRKWHWKKHE KCFVGSEMVN WLIRNFSDID TREDAIKYGQ KVMKEGLFVH VLNKHNFLDG HYFYQFSPEY VMDTN KLEK TNSHRSTLSD PKQMLRKAST GSSNDPSAMT PFSSVVPAIS ASNASVADAK EPSRPILMLS NSLVIDVDPA GKSSKQ ESC TVHYDRVHNP DHCFHIRLEW LTTTPKLIDD LVGNWSRLCE RYGLKMIEIP WEELCTIPSV NPFHSFVEIK LAINPWE DP EFKDRELFAK SKFYYHVYLL KASGFLLDNR ASKFLQNQDI EFDIMYSWGK PQFKYVQYIH HTGAYVAELR ENGCLFLA P NNIYISRVNP GNIIGKIHSA SSSSLDAQKV ILNFKSTCLD YQKLRSIFLD AKEMWITGKI VED

UniProtKB: Vacuolar membrane-associated protein IML1

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Macromolecule #7: Protein MEH1

MacromoleculeName: Protein MEH1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.266086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGAVLSCCRN HSGEENEALL REQQAGYGSQ GNANDEYDAE QMRLKEHEHE QKLLAREQEL RDIVANTNDK LIDISMINNS GIVIQGTDL QEALDKRQQE EGGDSREDER SAGDDNLSGH SVPSSGSAQA TTHQTAPRTN TFTLLTSPDS AKISKEQLKK L HSNILNEI FSQSQVNKPG PLTVPF

UniProtKB: Protein MEH1

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Macromolecule #8: Protein EGO2

MacromoleculeName: Protein EGO2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.104935 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEAEKQSDIK GTIAFDTHGN VIESTGVGSQ RIEDIGDLSK VTLDAEGFAQ VQGDSLLVHL YKRNDITLAV YTSAQ

UniProtKB: Protein EGO2

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Macromolecule #9: Protein SLM4

MacromoleculeName: Protein SLM4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.371877 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVMLHSKNVK GFLENTLKPY DLHSVDFKTS SLQSSMIITA TNGGILSYAT SNNDVPKNSI NEINSVNNLK MMSLLIKDKW SEDENDTEE QHSNSCYPVE IDSFKTKIYT YEMEDLHTCV AQIPNSDLLL LFIAEGSFPY GLLVIKIERA MRELTDLFGY K LG

UniProtKB: Protein SLM4

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 11 / Number of copies: 1 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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Macromolecule #12: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133077
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

8ae6

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model

6jwp

source_name: PDB, initial_model_type: experimental model
Output model

PDB-9h4q:
Cryo-EM structure of the SEAC wing - EGOC

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