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- EMDB-51887: Cryo-EM structure of the SEAC-EGOC supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-51887
TitleCryo-EM structure of the SEAC-EGOC supercomplex
Map dataComposite map
Sample
  • Complex: SEAC-EGOC supercomplex
    • Complex: SEA complex
      • Protein or peptide: x 8 types
    • Complex: EGO complex
      • Protein or peptide: x 5 types
  • Ligand: x 4 types
KeywordsCell growth / GTPase activating protein / GTPase / coatomer complex / SIGNALING PROTEIN
Function / homology
Function and homology information


MTOR signalling / GATOR1 complex / pseudohyphal growth / GATOR2 complex / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / positive regulation of ER to Golgi vesicle-mediated transport / Ragulator complex / microautophagy ...MTOR signalling / GATOR1 complex / pseudohyphal growth / GATOR2 complex / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / positive regulation of ER to Golgi vesicle-mediated transport / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / Amino acids regulate mTORC1 / proline transport / COPII-mediated vesicle transport / regulation of TORC1 signaling / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / COPII vesicle coat / Regulation of HSF1-mediated heat shock response / phosphate ion transport / regulation of autophagosome assembly / TORC1 signaling / SUMOylation of SUMOylation proteins / fungal-type vacuole / endocytic recycling / structural constituent of nuclear pore / vacuolar acidification / fungal-type vacuole membrane / SUMOylation of RNA binding proteins / negative regulation of TOR signaling / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / vacuolar membrane / nucleocytoplasmic transport / transcription by RNA polymerase III / positive regulation of macroautophagy / regulation of receptor recycling / positive regulation of TOR signaling / mRNA transport / nuclear pore / subtelomeric heterochromatin formation / transcription by RNA polymerase I / negative regulation of TORC1 signaling / ERAD pathway / 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 / cell periphery / meiotic cell cycle / cellular response to amino acid stimulus / protein import into nucleus / late endosome membrane / nuclear envelope / late endosome / protein transport / cellular response to oxidative stress / nuclear membrane / 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 / endoplasmic reticulum membrane / chromatin / GTP binding / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / 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 / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family ...YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid / : / : / 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 / 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 / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / 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
SEH-associated protein 4 / Protein SLM4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / Nucleoporin SEH1 / GTP-binding protein GTR2 / GTP-binding protein GTR1 / Protein MEH1 / Maintenance of telomere capping protein 5 ...SEH-associated protein 4 / Protein SLM4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / Nucleoporin SEH1 / GTP-binding protein GTR2 / GTP-binding protein GTR1 / Protein MEH1 / Maintenance of telomere capping protein 5 / Protein transport protein SEC13 / Restriction of telomere capping protein 1 / Protein EGO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 22, 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_51887.png

Downloads & links

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Map

FileDownload / File: emd_51887.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite 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: 0.0426
Minimum - Maximum0.0 - 1.5459057
Average (Standard dev.)0.0025862888 (±0.031526603)
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: Sea2-N-terminal-Seh1 focused map

Fileemd_51887_additional_1.map
AnnotationSea2-N-terminal-Seh1 focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sea2-Seh1-Sea3-Sec13 focused map

Fileemd_51887_additional_2.map
AnnotationSea2-Seh1-Sea3-Sec13 focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Monomer-focused map

Fileemd_51887_additional_3.map
AnnotationMonomer-focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Wing-focused map

Fileemd_51887_additional_4.map
AnnotationWing-focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus map where focused maps were fitted

Fileemd_51887_additional_5.map
AnnotationConsensus map where focused maps were fitted
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sea3-Sec13 focused map

Fileemd_51887_additional_6.map
AnnotationSea3-Sec13 focused 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 : SEAC-EGOC supercomplex

EntireName: SEAC-EGOC supercomplex
Components
  • Complex: SEAC-EGOC supercomplex
    • Complex: SEA complex
      • Protein or peptide: Maintenance of telomere capping protein 5
      • Protein or peptide: Protein transport protein SEC13
      • Protein or peptide: Restriction of telomere capping protein 1
      • Protein or peptide: SEH-associated protein 4
      • Protein or peptide: Nucleoporin SEH1
      • 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: ZINC ION
  • 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-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: SEA complex

SupramoleculeName: SEA complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5, #4, #8-#10
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: #6-#7, #11-#13
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: 2 / 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: Protein transport protein SEC13

MacromoleculeName: Protein transport protein SEC13 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Protein transport protein SEC13

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Macromolecule #3: Restriction of telomere capping protein 1

MacromoleculeName: Restriction of telomere capping protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Restriction of telomere capping protein 1

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Macromolecule #4: Nucleoporin SEH1

MacromoleculeName: Nucleoporin SEH1 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: Nucleoporin SEH1

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Macromolecule #5: SEH-associated protein 4

MacromoleculeName: SEH-associated protein 4 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (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

UniProtKB: SEH-associated protein 4

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Macromolecule #6: GTP-binding protein GTR1

MacromoleculeName: GTP-binding protein GTR1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / 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 #7: GTP-binding protein GTR2

MacromoleculeName: GTP-binding protein GTR2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #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: 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

+
Macromolecule #9: Nitrogen permease regulator 3

MacromoleculeName: Nitrogen permease regulator 3 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / 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

+
Macromolecule #10: Vacuolar membrane-associated protein IML1

MacromoleculeName: Vacuolar membrane-associated protein IML1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / 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

+
Macromolecule #11: Protein MEH1

MacromoleculeName: Protein MEH1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / 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

+
Macromolecule #12: Protein EGO2

MacromoleculeName: Protein EGO2 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / 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

+
Macromolecule #13: Protein SLM4

MacromoleculeName: Protein SLM4 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / 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

+
Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 28 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #16: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 16 / Number of copies: 2 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

+
Macromolecule #17: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 4 / 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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 208039
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

8adl

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-9h5k:
Cryo-EM structure of the SEAC-EGOC supercomplex

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