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- EMDB-15364: Cryo-EM structure of the SEA complex (consensus map) -

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Basic information

Entry
Database: EMDB / ID: EMD-15364
TitleCryo-EM structure of the SEA complex (consensus map)
Map dataDeepEMhancer sharpened map (wide mask)
Sample
  • Complex: Seh1-associated complex (SEAC)
    • Protein or peptide: Maintenance of telomere capping protein 5
    • Protein or peptide: Nucleoporin SEH1
    • Protein or peptide: SEH-associated protein 4
    • Protein or peptide: Protein transport protein SEC13Protein targeting
    • Protein or peptide: Restriction of telomere capping protein 1
    • Protein or peptide: Nitrogen permease regulator 3
    • Protein or peptide: Vacuolar membrane-associated protein IML1
    • Protein or peptide: Nitrogen permease regulator 2
  • Ligand: ZINC ION
Function / homology
Function and homology information


urea transport / GATOR1 complex / negative regulation of small GTPase mediated signal transduction / GATOR2 complex / pseudohyphal growth / proline transport / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding ...urea transport / GATOR1 complex / negative regulation of small GTPase mediated signal transduction / GATOR2 complex / pseudohyphal growth / proline transport / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / regulation of autophagosome assembly / COPII vesicle coat / TORC1 signaling / positive regulation of protein exit from endoplasmic reticulum / fungal-type vacuole / negative regulation of TOR signaling / structural constituent of nuclear pore / fungal-type vacuole membrane / nucleocytoplasmic transport / vacuolar membrane / positive regulation of macroautophagy / positive regulation of TOR signaling / mRNA transport / signaling adaptor activity / positive regulation of autophagy / nuclear pore / : / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / meiotic cell cycle / cell periphery / positive regulation of GTPase activity / protein import into nucleus / protein transport / nuclear envelope / nuclear membrane / intracellular signal transduction / response to xenobiotic stimulus / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / metal ion binding / cytosol / cytoplasm
Similarity search - Function
WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / Zinc-ribbon like family / 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 ...WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / Zinc-ribbon like family / 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 / DEPDC5 protein C-terminal region / RWD domain / RWD domain profile. / RWD / Sec13/Seh1 family / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SEH-associated protein 4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / Nucleoporin SEH1 / Maintenance of telomere capping protein 5 / Protein transport protein SEC13 / Restriction of telomere capping protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsTafur L / Loewith R
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 79-2019European Union
European Research Council (ERC)TENDOEuropean Union
CitationJournal: Nature / Year: 2022
Title: Cryo-EM structure of the SEA complex.
Authors: Lucas Tafur / Kerstin Hinterndorfer / Caroline Gabus / Chiara Lamanna / Ariane Bergmann / Yashar Sadian / Farzad Hamdi / Fotis L Kyrilis / Panagiotis L Kastritis / Robbie Loewith /
Abstract: The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in ...The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in yeast. Functionally, the SEAC has been divided into two subcomplexes: SEACIT, which has GAP activity and inhibits TORC1, and SEACAT, which regulates SEACIT. This system is conserved in mammals: the GATOR complex, consisting of GATOR1 (SEACIT) and GATOR2 (SEACAT), transmits amino acid and glucose signals to mTORC1. Despite its importance, the structure of SEAC/GATOR, and thus molecular understanding of its function, is lacking. Here, we solve the cryo-EM structure of the native eight-subunit SEAC. The SEAC has a modular structure in which a COPII-like cage corresponding to SEACAT binds two flexible wings, which correspond to SEACIT. The wings are tethered to the core via Sea3, which forms part of both modules. The GAP mechanism of GATOR1 is conserved in SEACIT, and GAP activity is unaffected by SEACAT in vitro. In vivo, the wings are essential for recruitment of the SEAC to the vacuole, primarily via the EGO complex. Our results indicate that rather than being a direct inhibitor of SEACIT, SEACAT acts as a scaffold for the binding of TORC1 regulators.
History
DepositionJul 8, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15364.png

Downloads & links

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Map

FileDownload / File: emd_15364.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map (wide mask)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 640 pix.
= 464.64 Å		0.73 Å/pix.
x 640 pix.
= 464.64 Å		0.73 Å/pix.
x 640 pix.
= 464.64 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0039863624 - 2.4169307
Average (Standard dev.)0.0031031012 (±0.036953777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 464.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15364_msk_1.map
Projections & Slices
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Additional map: Unsharpened map

Fileemd_15364_additional_1.map
AnnotationUnsharpened map
Projections & Slices
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Additional map: DeepEMhancer sharpened map (tight mask)

Fileemd_15364_additional_2.map
AnnotationDeepEMhancer sharpened map (tight mask)
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_15364_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_15364_half_map_2.map
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Sample components

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Entire : Seh1-associated complex (SEAC)

EntireName: Seh1-associated complex (SEAC)
Components
  • Complex: Seh1-associated complex (SEAC)
    • Protein or peptide: Maintenance of telomere capping protein 5
    • Protein or peptide: Nucleoporin SEH1
    • Protein or peptide: SEH-associated protein 4
    • Protein or peptide: Protein transport protein SEC13Protein targeting
    • Protein or peptide: Restriction of telomere capping protein 1
    • Protein or peptide: Nitrogen permease regulator 3
    • Protein or peptide: Vacuolar membrane-associated protein IML1
    • Protein or peptide: Nitrogen permease regulator 2
  • Ligand: ZINC ION

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Supramolecule #1: Seh1-associated complex (SEAC)

SupramoleculeName: Seh1-associated complex (SEAC) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.09 MDa

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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Macromolecule #2: Nucleoporin SEH1

MacromoleculeName: Nucleoporin SEH1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 39.170758 KDa
SequenceString: MQPFDSGHDD LVHDVVYDFY GRHVATCSSD QHIKVFKLDK DTSNWELSDS WRAHDSSIVA IDWASPEYGR IIASASYDKT VKLWEEDPD QEECSGRRWN KLCTLNDSKG SLYSVKFAPA HLGLKLACLG NDGILRLYDA LEPSDLRSWT LTSEMKVLSI P PANHLQSD ...String:
MQPFDSGHDD LVHDVVYDFY GRHVATCSSD QHIKVFKLDK DTSNWELSDS WRAHDSSIVA IDWASPEYGR IIASASYDKT VKLWEEDPD QEECSGRRWN KLCTLNDSKG SLYSVKFAPA HLGLKLACLG NDGILRLYDA LEPSDLRSWT LTSEMKVLSI P PANHLQSD FCLSWCPSRF SPEKLAVSAL EQAIIYQRGK DGKLHVAAKL PGHKSLIRSI SWAPSIGRWY QLIATGCKDG RI RIFKITE KLSPLASEES LTNSNMFDNS ADVDMDAQGR SDSNTEEKAE LQSNLQVELL SEHDDHNGEV WSVSWNLTGT ILS SAGDDG KVRLWKATYS NEFKCMSVIT AQQ

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Macromolecule #3: SEH-associated protein 4

MacromoleculeName: SEH-associated protein 4 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 117.77575 KDa
SequenceString: MGLIKKVTHW SYDNLIDYLS VNPTRDEVTH YKVDPENESD ESIIKLHTVK DFGSITCLDY SESEIGMIGV GEKNGYLRIF NISGQNSSS PASHAPVGLN ANNETSMTNA SGGKAAQAEN IVGSVSNLKD TQGYPVSETN YDIRVRAKKQ RCINSLGINT N GLIAMGLD ...String:
MGLIKKVTHW SYDNLIDYLS VNPTRDEVTH YKVDPENESD ESIIKLHTVK DFGSITCLDY SESEIGMIGV GEKNGYLRIF NISGQNSSS PASHAPVGLN ANNETSMTNA SGGKAAQAEN IVGSVSNLKD TQGYPVSETN YDIRVRAKKQ RCINSLGINT N GLIAMGLD RNKHDSSLQI WDMNYHDDSH ETINPMFSYC TNESIVSLKF LNDTSVLAAS TKFLKEIDVR SPNPIYQHPT RL TYDIKLN PFNDWQFSTY GDDGTLAIWD RRKLSDQASL GDLNVASPLL TFEKLVGSGA ASRKYMNSCF RWSCVRNNEF ATL HRGDTI KRWRLGYYCD SNRDIAADDD NEMNIENLFV SSVHDTNTMY DRVATFDYIP RSNNGTSLIC MRQSGTIYRM PISE VCSKA ILNNRNSLLL SNFENTEIDE IRVNNEHEKS NLENVKTILK NLSFEDLDVS EDYFPSGHDE PNNEIEYSEL SEEEN EGSN DVLDSKRGFE LFWKPEKLLE KDISVIMRTR ASLGYGLDPM NTVEMIDSSK NLQNNAYIRN TWRWIAIAKA SVDDGT MVS GDLDLGYEGV IGIWNGINGI SNQDRYRQET ILSDKQLNKE MEKIIKLRRK NRDRNSPIAN AAGSPKYVQR RLCLIIS GW DLSRSDYEDK YNIIMKNGHY EKAAAWAVFF GDIPKAVEIL GSAKKERLRL IATAIAGYLA YKDLPGNNAW RQQCRKMS S ELDDPYLRVI FAFIADNDWW DILYEPAISL RERLGVALRF LNDTDLTTFL DRTSSTVIEN GELEGLILTG ITPNGIDLL QSYVNKTSDV QSAALISIFG SPRYFRDQRV DEWIQTYRDM LKSWELFSMR ARFDVLRSKL SRTKTGVLTA DIKPRQIYIQ CQNCKQNIN TPRTSSPSSA VSTSAGNYKN GEAYRRNNAD YKKFNTGSSE AQAADEKPRH KYCCPHCGSS FPRCAICLMP L GTSNLPFV INGTQSRDPM QTEDSQDGAN RELVSRKLKL NEWFSFCLSC NHGMHAGHAE EWFDRHNVCP TPGCTCQCNK

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Macromolecule #4: Protein transport protein SEC13

MacromoleculeName: Protein transport protein SEC13 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 33.082965 KDa
SequenceString: MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA SSDGKVSVVE FKENGTTSPI IIDAHAIGVN SASWAPATIE E DGEHNGTK ...String:
MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA SSDGKVSVVE FKENGTTSPI IIDAHAIGVN SASWAPATIE E DGEHNGTK ESRKFVTGGA DNLVKIWKYN SDAQTYVLES TLEGHSDWVR DVAWSPTVLL RSYLASVSQD RTCIIWTQDN EQ GPWKKTL LKEEKFPDVL WRASWSLSGN VLALSGGDNK VTLWKENLEG KWEPAGEVHQ

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Macromolecule #5: Restriction of telomere capping protein 1

MacromoleculeName: Restriction of telomere capping protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 149.533297 KDa
SequenceString: MSLSPHVENA SIPKGSTPIP KNRNVSSIGK GEFLGSSSSN NSSFRMNHYS NSGQPSVLDS IRRPNLTPTF SYSNGVYMPE SHRTSSFND SYLPYDKNPY AKTTGSMSNK SNMKIKTKKN AINTNTRKSS GLIYTTKVDK ELSSIDKVND PNINGLVCAG K THLGLYKF ...String:
MSLSPHVENA SIPKGSTPIP KNRNVSSIGK GEFLGSSSSN NSSFRMNHYS NSGQPSVLDS IRRPNLTPTF SYSNGVYMPE SHRTSSFND SYLPYDKNPY AKTTGSMSNK SNMKIKTKKN AINTNTRKSS GLIYTTKVDK ELSSIDKVND PNINGLVCAG K THLGLYKF SPSDRSIKCV HDFITPNSNT STRGTTSLLP KLSKRTRQNK FSTIADVKTG FNNYKNCIAV CNNSTAISIY DL NKSSSID NPLITSLCEH TRSINSFDFN MVESNLIISG GQDSCVKIWD LRSNKSKSSN RSDISINTAS DSIRDVKWMP GYN FASKND QGSSTYGNLK SGYKFASIHD SGYLLKFDLR QPAQYEKKLN AHTGPGLCLN WHPNQEYIAT GGRDGKCCLW FVGD NANAA ENTVLNYGNS PSLHAPNTSL NNSGSLAFPK LTINTGYPVT KLKFKPAYSS NIYNSLLGIS SMGDEAEVRI YSLAR KYIP KHVLLSETPS LGLVWWDENL IFNIDKGTRI NGWDINKEPT VLENLSKNTT TWRDLDGNGL LSVDQEIGSY EVVEPE LQP TSSTTCKKHP GTIKNPKNGN PENQGIIGGI KKGFSHTGLT SFTPERPPTL KAGPTFSTKS LTLASGASSF NSSSASL TS LTPQTENREE IAIEPPCIIT LDIPQIFNNI RLTKIAHSRK KNVISESSSM KNSPVEKFKY LARQLKFSYI REHNVSDS A DTAYKNDIEN IDVVKNATET HGDNTTTTNN NDDGDDDDDD DDDDKIIESH LLKKYNFPEN NTWATLMNEK VNNKKSKRN SSSSREFDEK DVRSSISSIS ASRQSHDRAR KIDKNVEAEL QEKIQTLVDL ISIATHNASV YLSIDDLTNF KIWILIRDSL LWDLKWMTS SQISSDNASN MDANESSDFE AGENLKTGKE FPEEDGAGTS GAESLVEERP QAFRANSDEP SDAEKKPVSK L KEQLKNTE IIPYAQPNED SDEVLTKLKE LQNQRLESRT KMGETVSDDV IIEEDEHEHQ EEEQPHDSPT KSAQFHASPI AK SIPILQK REHRKSFIDT FMLHSPNGYN GDTDIGNEDD NISPRFTYNS VSPRSKVSSL QSYATTTSQL ETFKKLSSHT API IGSPRH APSRPDSIGR EQLSSSLTKK LAKCKKIIAD PPWDTKKLIK QLYNQATETG NVVLTVNILF LFQTIYQITE IDIA KDAIA HFLLLLHRYE LFGIAADVLK YCPFEDIMGS EGDQSSIRLF CERCGELITN ESSKEKLRAE AQQTGNKKIM DKFGY WYCD SCKKKNTSCV LCERPLKKLT MVILPCGHEG HFQCIQEWFL DENEQECPGG CPGVAFI

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Macromolecule #6: Nitrogen permease regulator 3

MacromoleculeName: Nitrogen permease regulator 3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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Macromolecule #7: Vacuolar membrane-associated protein IML1

MacromoleculeName: Vacuolar membrane-associated protein IML1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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Macromolecule #8: Nitrogen permease regulator 2

MacromoleculeName: Nitrogen permease regulator 2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 28 / 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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio map
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Ab initio job / Details: Ab initio map
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Non-uniform refinement / Details: Non-uniform refinement
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 208379
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3f3f

chain_id: A

3mzk

chain_id: A
DetailsAlphaFold predictions were used as starting models for Sea1, Sea2, Sea3, Sea4, Npr2 and Npr3. Rigid body fit was performed in Chimera, and manual building in Coot.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8adl:
Cryo-EM structure of the SEA complex

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