[English] 日本語
Yorodumi
- EMDB-54223: Cryo-EM structure of the Target of Rapamycin Complex 2 (TORC2) wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54223
TitleCryo-EM structure of the Target of Rapamycin Complex 2 (TORC2) with the Avo1 PH domain
Map dataDeepEMhancer map
Sample
  • Complex: Target of Rapamycin Complex 2
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Serine/threonine-protein kinase TOR2
    • Protein or peptide: Target of rapamycin complex 2 subunit TSC11
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO2
    • Protein or peptide: Target of rapamycin complex 2 subunit BIT61
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO1
  • Ligand: INOSITOL HEXAKISPHOSPHATE
Keywordscell growth / metabolism / SIGNALING PROTEIN
Function / homology
Function and homology information


PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / TOR complex / regulation of snRNA pseudouridine synthesis / mitochondria-nucleus signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of TP53 Degradation / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment or maintenance of actin cytoskeleton polarity ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / TOR complex / regulation of snRNA pseudouridine synthesis / mitochondria-nucleus signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of TP53 Degradation / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / fungal-type cell wall organization / Amino acids regulate mTORC1 / TORC2 complex / TORC1 complex / sphingolipid biosynthetic process / TORC2 signaling / fungal-type vacuole membrane / cellular response to nitrogen starvation / vacuolar membrane / negative regulation of macroautophagy / positive regulation of Rho protein signal transduction / TORC1 signaling / TOR signaling / positive regulation of endocytosis / protein-membrane adaptor activity / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / response to nutrient / nuclear periphery / guanyl-nucleotide exchange factor activity / negative regulation of autophagy / protein serine/threonine kinase activator activity / cell periphery / protein localization to plasma membrane / regulation of actin cytoskeleton organization / regulation of cell growth / ribosome biogenesis / molecular adaptor activity / non-specific serine/threonine protein kinase / endosome membrane / regulation of cell cycle / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TORC2 component Bit61/PRR5 / HbrB-like / : / AVO1 ubiquitin-like domain / Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, domain 4 / Rapamycin-insensitive companion of mTOR RasGEF_N domain ...TORC2 component Bit61/PRR5 / HbrB-like / : / AVO1 ubiquitin-like domain / Rapamycin-insensitive companion of mTOR, N-terminal domain / Pianissimo family / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR, domain 4 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, domain 5 / Rapamycin-insensitive companion of mTOR RasGEF_N domain / Rapamycin-insensitive companion of mTOR, middle domain / Rapamycin-insensitive companion of mTOR, N-term / Rapamycin-insensitive companion of mTOR, domain 5 / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / PH-like domain superfamily / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase TOR2 / Target of rapamycin complex 2 subunit TSC11 / Target of rapamycin complex subunit LST8 / Target of rapamycin complex 2 subunit BIT61 / Target of rapamycin complex 2 subunit AVO2 / Target of rapamycin complex 2 subunit AVO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsTafur L / Zou L / Loewith R
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
CitationJournal: Mol Cell / Year: 2026
Title: Structural basis for TORC2 activation.
Authors: Luoming Zou / Maria G Tettamanti / Caroline Gabus / Ariane Bergmann / Robbie Loewith / Lucas Tafur /
Abstract: The target of rapamycin complex 2 (TORC2) is a central node in signaling feedback loops, serving to maintain the biophysical homeostasis of the plasma membrane (PM). How TORC2 is regulated by ...The target of rapamycin complex 2 (TORC2) is a central node in signaling feedback loops, serving to maintain the biophysical homeostasis of the plasma membrane (PM). How TORC2 is regulated by mechanical perturbation of the PM is not well understood. To address this, we determined the cryo-electron microscopy structure of endogenous yeast TORC2 at up to 2.2 Å resolution. Our model refines the position and interactions of TORC2-specific subunits, providing a structural basis for the differential assembly of Tor2 into TORC2. Furthermore, we observe the insertion of the pleckstrin-homology domain of the Avo1 subunit into the Tor2 active site, providing a regulatory mechanism mediated by phosphoinositides. Structure-guided functional experiments reveal a potential TORC2 membrane-binding surface and a positively charged pocket in the Avo3 subunit that is necessary for TORC2 activation. Collectively, our data suggest that signaling phosphoinositides activate TORC2 by membrane-induced structural rearrangements via the concerted action of conserved regulatory subunits.
History
DepositionJul 1, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54223.png

Downloads & links

-
Map

FileDownload / File: emd_54223.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 512 pix.
= 464.896 Å		0.91 Å/pix.
x 512 pix.
= 464.896 Å		0.91 Å/pix.
x 512 pix.
= 464.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.908 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.061
Minimum - Maximum-0.0016444394 - 1.9712945
Average (Standard dev.)0.0021853102 (±0.03366451)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 464.896 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_54223_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54223_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54223_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Target of Rapamycin Complex 2

EntireName: Target of Rapamycin Complex 2
Components
  • Complex: Target of Rapamycin Complex 2
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Serine/threonine-protein kinase TOR2
    • Protein or peptide: Target of rapamycin complex 2 subunit TSC11
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO2
    • Protein or peptide: Target of rapamycin complex 2 subunit BIT61
    • Protein or peptide: Target of rapamycin complex 2 subunit AVO1
  • Ligand: INOSITOL HEXAKISPHOSPHATE

-
Supramolecule #1: Target of Rapamycin Complex 2

SupramoleculeName: Target of Rapamycin Complex 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Target of rapamycin complex subunit LST8

MacromoleculeName: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.077879 KDa
SequenceString: MSVILVSAGY DHTIRFWEAL TGVCSRTIQH SDSQVNRLEI TNDKKLLATA GHQNVRLYDI RTTNPNPVAS FEGHRGNVTS VSFQQDNRW MVTSSEDGTI KVWDVRSPSI PRNYKHNAPV NEVVIHPNQG ELISCDRDGN IRIWDLGENQ CTHQLTPEDD T SLQSLSMA ...String:
MSVILVSAGY DHTIRFWEAL TGVCSRTIQH SDSQVNRLEI TNDKKLLATA GHQNVRLYDI RTTNPNPVAS FEGHRGNVTS VSFQQDNRW MVTSSEDGTI KVWDVRSPSI PRNYKHNAPV NEVVIHPNQG ELISCDRDGN IRIWDLGENQ CTHQLTPEDD T SLQSLSMA SDGSMLAAAN TKGNCYVWEM PNHTDASHLK PVTKFRAHST YITRILLSSD VKHLATCSAD HTARVWSIDD DF KLETTLD GHQRWVWDCA FSADSAYLVT ASSDHYVRLW DLSTREIVRQ YGGHHKGAVC VALNDV

UniProtKB: Target of rapamycin complex subunit LST8

-
Macromolecule #2: Serine/threonine-protein kinase TOR2

MacromoleculeName: Serine/threonine-protein kinase TOR2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 281.915438 KDa
SequenceString: MNKYINKYTT PPNLLSLRQR AEGKHRTRKK LTHKSHSHDD EMSTTSNTDS NHNGPNDSGR VITGSAGHIG KISFVDSELD TTFSTLNLI FDKLKSDVPQ ERASGANELS TTLTSLAREV SAEQFQRFSN SLNNKIFELI HGFTSSEKIG GILAVDTLIS F YLSTEELP ...String:
MNKYINKYTT PPNLLSLRQR AEGKHRTRKK LTHKSHSHDD EMSTTSNTDS NHNGPNDSGR VITGSAGHIG KISFVDSELD TTFSTLNLI FDKLKSDVPQ ERASGANELS TTLTSLAREV SAEQFQRFSN SLNNKIFELI HGFTSSEKIG GILAVDTLIS F YLSTEELP NQTSRLANYL RVLIPSSDIE VMRLAANTLG RLTVPGGTLT SDFVEFEVRT CIDWLTLTAD NNSSSSKLEY RR HAALLII KALADNSPYL LYPYVNSILD NIWVPLRDAK LIIRLDAAVA LGKCLTIIQD RDPALGKQWF QRLFQGCTHG LSL NTNDSV HATLLVFREL LSLKAPYLRD KYDDIYKSTM KYKEYKFDVI RREVYAILPL LAAFDPAIFT KKYLDRIMVH YLRY LKNID MNAANNSDKP FILVSIGDIA FEVGSSISPY MTLILDNIRE GLRTKFKVRK QFEKDLFYCI GKLACALGPA FAKHL NKDL LNLMLNCPMS DHMQETLMIL NEKIPSLEST VNSRILNLLS ISLSGEKFIQ SNQYDFNNQF SIEKARKSRN QSFMKK TGE SNDDITDAQI LIQCFKMLQL IHHQYSLTEF VRLITISYIE HEDSSVRKLA ALTSCDLFIK DDICKQTSVH ALHSVSE VL SKLLMIAITD PVAEIRLEIL QHLGSNFDPQ LAQPDNLRLL FMALNDEIFG IQLEAIKIIG RLSSVNPAYV VPSLRKTL L ELLTQLKFSN MPKKKEESAT LLCTLINSSD EVAKPYIDPI LDVILPKCQD ASSAVASTAL KVLGELSVVG GKEMTRYLK ELMPLIINTF QDQSNSFKRD AALTTLGQLA ASSGYVVGPL LDYPELLGIL INILKTENNP HIRRGTVRLI GILGALDPYK HREIEVTSN SKSSVEQNAP SIDIALLMQG VSPSNDEYYP TVVIHNLMKI LNDPSLSIHH TAAIQAIMHI FQNLGLRCVS F LDQIIPGI ILVMRSCPPS QLDFYFQQLG SLISIVKQHI RPHVEKIYGV IREFFPIIKL QITIISVIES ISKALEGEFK RF VPETLTF FLDILENDQS NKRIVPIRIL KSLVTFGPNL EDYSHLIMPI VVRMTEYSAG SLKKISIITL GRLAKNINLS EMS SRIVQA LVRILNNGDR ELTKATMNTL SLLLLQLGTD FVVFVPVINK ALLRNRIQHS VYDQLVNKLL NNECLPTNII FDKE NEVPE RKNYEDEMQV TKLPVNQNIL KNAWYCSQQK TKEDWQEWIR RLSIQLLKES PSACLRSCSS LVSVYYPLAR ELFNA SFSS CWVELQTSYQ EDLIQALCKA LSSSENPPEI YQMLLNLVEF MEHDDKPLPI PIHTLGKYAQ KCHAFAKALH YKEVEF LEE PKNSTIEALI SINNQLHQTD SAIGILKHAQ QHNELQLKET WYEKLQRWED ALAAYNEKEA AGEDSVEVMM GKLRSLY AL GEWEELSKLA SEKWGTAKPE VKKAMAPLAA GAAWGLEQWD EIAQYTSVMK SQSPDKEFYD AILCLHRNNF KKAEVHIF N ARDLLVTELS ALVNESYNRA YNVVVRAQII AELEEIIKYK KLPQNSDKRL TMRETWNTRL LGCQKNIDVW QRILRVRSL VIKPKEDAQV RIKFANLCRK SGRMALAKKV LNTLLEETDD PDHPNTAKAS PPVVYAQLKY LWATGLQDEA LKQLINFTSR MAHDLGLDP NNMIAQSVPQ QSKRVPRHVE DYTKLLARCF LKQGEWRVCL QPKWRLSNPD SILGSYLLAT HFDNTWYKAW H NWALANFE VISMLTSVSK KKQEGSDASS VTDINEFDNG MIGVNTFDAK EVHYSSNLIH RHVIPAIKGF FHSISLSESS SL QDALRLL TLWFTFGGIP EATQAMHEGF NLIQIGTWLE VLPQLISRIH QPNQIVSRSL LSLLSDLGKA HPQALVYPLM VAI KSESLS RQKAALSIIE KMRIHSPVLV DQAELVSHEL IRMAVLWHEQ WYEGLDDASR QFFGEHNTEK MFAALEPLYE MLKR GPETL REISFQNSFG RDLNDAYEWL MNYKKSKDVS NLNQAWDIYY NVFRKIGKQL PQLQTLELQH VSPKLLSAHD LELAV PGTR ASGGKPIVKI SKFEPVFSVI SSKQRPRKFC IKGSDGKDYK YVLKGHEDIR QDSLVMQLFG LVNTLLQNDA ECFRRH LDI QQYPAIPLSP KSGLLGWVPN SDTFHVLIRE HREAKKIPLN IEHWVMLQMA PDYDNLTLLQ KVEVFTYALN NTEGQDL YK VLWLKSRSSE TWLERRTTYT RSLAVMSMTG YILGLGDRHP SNLMLDRITG KVIHIDFGDC FEAAILREKF PEKVPFRL T RMLTYAMEVS GIEGSFRITC ENVMKVLRDN KGSLMAILEA FAFDPLINWG FDLPTKKIEE ETGIQLPVMN ANELLSNGA ITEEEVQRVE NEHKNAIRNA RAMLVLKRIT DKLTGNDIRR FNDLDVPEQV DKLIQQATSV ENLCQHYIGW CPFW

UniProtKB: Serine/threonine-protein kinase TOR2

-
Macromolecule #3: Target of rapamycin complex 2 subunit TSC11

MacromoleculeName: Target of rapamycin complex 2 subunit TSC11 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 164.580609 KDa
SequenceString: MSIPHSAKQS SPLSSRRRSV TNTTPLLTPR HSRDNSSTQI SSAKNITSSS PSTITNESSK RNKQNLVLST SFISTKRLEN SAPSPTSPL MARRTRSTMT KALLNLKAEI NNQYQELARL RKKKDDIEHL RDSTISDIYS GSYSTNHLQK HSMRIRANTQ L REIDNSIK ...String:
MSIPHSAKQS SPLSSRRRSV TNTTPLLTPR HSRDNSSTQI SSAKNITSSS PSTITNESSK RNKQNLVLST SFISTKRLEN SAPSPTSPL MARRTRSTMT KALLNLKAEI NNQYQELARL RKKKDDIEHL RDSTISDIYS GSYSTNHLQK HSMRIRANTQ L REIDNSIK RVEKHIFDLK QQFDKKRQRS LTTSSSIKAD VGSIRNDDGQ NNDSEELGDH DSLTDQVTLD DEYLTTPTSG TE RNSQQNL NRNSTVNSRN NENHSTLSIP DLDGSNKVNL TGDTEKDLGD LENENQIFTS TTTEAATWLV SDYMQSFQEK NVN PDFIAQ KANGLVTLLK EHSEIRKDLV LTSFMSSIQN LLLNGNKLIA ASAYRVCRYL INSSIFIDEL LELRLDAFII ISLA KDNSF QIEREQALKM VRRFIEYNNG VTQGIMQAII SCVEKPEDSL RHMALETLLE LCFVAPEMVK ECRGMRVIEG FLQDY TSFS LASVILDTIL QLMATHKTRQ HFLEDFNVSV LTTVFSDTNT KSNVNVEKMQ NASTLISITL NSYNGFMLFS NNNFKP LKQ LVSFFQIPIC AQYLIDIFLD VLKIKPLPYK PRGRHSHSFK PIPSQYYKEC MSVNQRLALI VLILENSEFV PHLLELL NE EDRDDHLVAK GRYLLTEYFN LRMNLVDKKY TSVSKPIYKE NFTYVNETFQ FKKIAYKMNR NRNTIGMSGI DYAQNIKS F SKNIKENTLL REVDDFRFRR MVYDSKVLQT KDFTRWNWNI INELLEGPLL NKKQLEELVK STKFIRRLLV FYRPLRLRF SNVNKGAKLS QKYVQVGCQF FKTLTATPEG MKILMDDTKI IPQLASLMFR AMEGNISGNI FNKNKLREKI IFGYFKFIGI LTQSKNGVH ILTRWNFFTV IYKMFQFESK LGLEFLLLTI PELDLKYSSH CRVIIGKALV VANEKVRIEA TKHIGDKLKE L LSTKESDL KLKANKVKLQ QFKMEMLTRQ LYDLSPSVVA VADQALYECI VAGNGSEELG TSFRMFLNQM VFIRSPILFE LL SRPYGFQ LLNEINFVKE ERDSWLSKKN IEYVHIVEEF LKKNESINAK SLTFQQKSRL PLHFYESLTK TEDGILLLSQ TGD LVTFMN VIKKYVNGNN MATVENAKEI LDLKAALWCV GFIGSTELGI GLLDNYSLVE DIIEVAYNAS VTSVRFTAFY VLGL ISMTR EGCEILDEMG WNCCVSVQDE PIGIALPNRL DRFLSYNEHK WSAFGEYSDE MIVFNKSDGD LIEKCLPIEF DLDKL LKEK DTAENPLNEK IITNKYDNDI TSQTITVSGE NSSLFANEGL SSPYVTQYRN DDDSIESKVL HIVSQLGNHI LSNHAV KEI TEINNKYGPR LFENEKMFFK VFNMMSKYRF KPHVRKFLCG LFINNRALEN VIRHDNKRDK RPANFTR

UniProtKB: Target of rapamycin complex 2 subunit TSC11

-
Macromolecule #4: Target of rapamycin complex 2 subunit AVO2

MacromoleculeName: Target of rapamycin complex 2 subunit AVO2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.206457 KDa
SequenceString: MLKEPSVRLR EAIIEGNLLI VKRLLRRNPD LLTNIDSENG WSSLHYASYH GRYLICVYLI QLGHDKHELI KTFKGNTCVH LALMKGHEQ TLHLLLQQFP RFINHRGENG RAPIHIACMN DYYQCLSLLI GVGADLWVMD TNGDTPLHVC LEYGSISCMK M LLNEGEVS ...String:
MLKEPSVRLR EAIIEGNLLI VKRLLRRNPD LLTNIDSENG WSSLHYASYH GRYLICVYLI QLGHDKHELI KTFKGNTCVH LALMKGHEQ TLHLLLQQFP RFINHRGENG RAPIHIACMN DYYQCLSLLI GVGADLWVMD TNGDTPLHVC LEYGSISCMK M LLNEGEVS LDDNVRDKGN WKPIDVAQTF EVGNIYSKVL KEVKKKGPPL GAGKKPSSFR TPILNAKATF EDGPSPVLSM NS PYSLYSN NSPLPVLPRR ISTHTTSGNG GNRRSSITNP VFNPRKPTLS TDSFSSSSNS SSRLRVNSIN VKTPVGVSPK KEL VSESVR HSATPTSPHN NIALINRYLL PNKSNDNVRG DSQTATINDD GGGGNGGDAT IGMGLRKDPD DENENKYKIK VNNG EPRRR VSLLNIPISK LRNSNNTRAE D

UniProtKB: Target of rapamycin complex 2 subunit AVO2

-
Macromolecule #5: Target of rapamycin complex 2 subunit BIT61

MacromoleculeName: Target of rapamycin complex 2 subunit BIT61 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 60.908676 KDa
SequenceString: MTAEDILLRE RTSTTTQRPV NSEQYLNVQL ATAPVKNFQT TSEISRQTLV DTSNDDVYSI KNLKGSRNPI SPSVSNVGFQ SIFHTVDHP RSKVSVASNH SLRSNDNASA ATSKSGSSQI GESHSVDTVE CSNNLSKKLS SDAISITQKS LHSTPSGRYM K GKASGFFN ...String:
MTAEDILLRE RTSTTTQRPV NSEQYLNVQL ATAPVKNFQT TSEISRQTLV DTSNDDVYSI KNLKGSRNPI SPSVSNVGFQ SIFHTVDHP RSKVSVASNH SLRSNDNASA ATSKSGSSQI GESHSVDTVE CSNNLSKKLS SDAISITQKS LHSTPSGRYM K GKASGFFN RRNRAHTTIS SDPASFLTDS STLHNSSHSF RNVIKNFFQN KSHRHIGQDA IEPAIPNSLS KFLHSSYGRH KS PSQFIHT NAGQLVDSGT SVYSLNVNPS GVNPNTIVED PLSGTDPASP NPVSMLHDLL RNLPSLEANY KHFNSQELTT LTN NIWNIF CSNVAELFRT QRIWKLRAKI ENFNEVLEFY CILKTDPRVT HSGMNRIISD LKEFLVSSLY NLENQIVFNY SNED TINNA LKRLGVIWRI FYQEVYYDLA AVLLPLDQSI REDGNSTVLK SGNESRTHIN GNYSIGFLLL MCFRDSIVLP CYENF VNSN DGISKSFQLY IFNQEEESNV TETDKLTLLQ CFGILSTIQS NDRNQRIIEE LLAGIRMSI

UniProtKB: Target of rapamycin complex 2 subunit BIT61

-
Macromolecule #6: Target of rapamycin complex 2 subunit AVO1

MacromoleculeName: Target of rapamycin complex 2 subunit AVO1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 131.565453 KDa
SequenceString: MDTVTVLNEL RAQFLRVCPE KDQMKRIIKP YIPVDEFNTE QCLDSSIREL YMNSDGVSLL PELESPPVSK DFMENYASLG KMRIMRENE GQKGKANQNL IGAEKTERDE EETRNLQDKS AKNTLIVEEN GTLRYNPLNS SASNSLLNDD DHTSGKHHKT S SKEDSYLN ...String:
MDTVTVLNEL RAQFLRVCPE KDQMKRIIKP YIPVDEFNTE QCLDSSIREL YMNSDGVSLL PELESPPVSK DFMENYASLG KMRIMRENE GQKGKANQNL IGAEKTERDE EETRNLQDKS AKNTLIVEEN GTLRYNPLNS SASNSLLNDD DHTSGKHHKT S SKEDSYLN SSMEMQKKSS KRSSLPFVRI FKSRRDHSNT SGNKNVMNTT NTRAKSSTLH PPGARHNKKG SKFDMNFDFD EN LEEEDDD DDDDEEGDDI HSQFFQLDDD FDAKGSGASP AHKGINGMSN NKNNTYTNNR NSISILDDRE SSNGNIGSAS RLK SHFPTS QKGKIFLTDN KNDGQKSDSL NANKGIHGDG SSASGNGSVS RDGLTETESN NISDMESYIN EKDLDDLNFD TVTS NINKT VSDLGGHEST NDGTAVMNRD SKDSRSNSNE FNAQNRDRIT PGSSYGKSLL GSEYSEERYS NNDSSTMESG EMSLD SDMQ TNTIPSHSIP MSMQKYGIYH GDDDSTLNNV FDKAVLTMNS SRHPKERRDT VISGKEPTSL TSSNRKFSVS SNLTST RSP LLRGHGRTSS TASSEHMKAP KVSDSVLHRA RKSTLTLKQD HSQPSVPSSV HKSSKEGNIL IEKTTDYLVS KPKASQL SN MFNKKKKRTN TNSVDVLEYF SFVCGDKVPN YESMGLEIYI QASKKYKRNS FTTKVRKSST IFEVIGFALF LYSTEKKP D NFEEDGLTVE DISNPNNFSL KIVDEDGEPF EDNFGKLDRK STIQSISDSE VVLCKVDDAE KSQNEIETPL PFETGGGLM DASTLDANSS HDTTDGTINQ LSFYKPIIGN EDDIDKTNGS KIIDVTVYLY PNVNPKFNYT TISVLVTSHI NDILVKYCKM KNMDPNEYA LKVLGKNYIL DLNDTVLRLD GINKVELISK KDARELHLEK MKPDLKKPVL PTIQSNDLTP LTLEPLNSYL K ADAGGAVA AIPENTKVTS KAKKISTKYK LGLAKQHSSS SVASGSVSTA GGLANGNGFF KNKNSSKSSL HGTLQFHNIN RS QSTMEHT PDTPNGVGDN FQDLFTGAYH KYKVWRRQQM SFINKHERTL AIDGDYIYIV PPEGRIHWHD NVKTKSLHIS QVV LVKKSK RVPEHFKIFV RREGQDDIKR YYFEAVSGQE CTEIVTRLQN LLSAYRMNHK

UniProtKB: Target of rapamycin complex 2 subunit AVO1

-
Macromolecule #7: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51729
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more