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- EMDB-72378: DEPDC5 dimer (tandem DEPDC5) focused map -

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Basic information

Entry
Database: EMDB / ID: EMD-72378
TitleDEPDC5 dimer (tandem DEPDC5) focused map
Map dataEMReady sharpened focused map
Sample
  • Complex: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
    • Protein or peptide: GATOR1 complex protein DEPDC5
KeywordsLysosome / GATOR1 / KICSTOR / cell growth / amino acid sensing / mTOR / KPTN / ITFG2 / C12orf66 / SZT2 / NPRL2 / NPRL3 / DEPDC5 / CELL CYCLE
Function / homology
Function and homology information


GATOR1 complex / Amino acids regulate mTORC1 / negative regulation of TORC1 signaling / positive regulation of autophagy / GTPase activator activity / cellular response to amino acid starvation / small GTPase binding / lysosome / intracellular signal transduction / lysosomal membrane ...GATOR1 complex / Amino acids regulate mTORC1 / negative regulation of TORC1 signaling / positive regulation of autophagy / GTPase activator activity / cellular response to amino acid starvation / small GTPase binding / lysosome / intracellular signal transduction / lysosomal membrane / protein-containing complex binding / perinuclear region of cytoplasm / cytosol
Similarity search - Function
: / IML1 N-terminal double psi beta barrel domain / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / Vacuolar membrane-associated protein Iml1, N-terminal domain / DEPDC5 protein C-terminal region / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin ...: / IML1 N-terminal double psi beta barrel domain / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / Vacuolar membrane-associated protein Iml1, N-terminal domain / DEPDC5 protein C-terminal region / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GATOR1 complex protein DEPDC5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBayly-Jones C / Lupton CJ / Chang YG / Ellisdon AM
Funding support Australia, 4 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2036864 Australia
Australian Research Council (ARC)DE240100992 Australia
Other governmentMCRF21036 Australia
Australian Research Council (ARC)LE170100016 Australia
CitationJournal: To Be Published
Title: Structure of the lysosomal KICSTOR-GATOR1 nutrient-sensing supercomplex
Authors: Bayly-Jones C / Lupton CJ / Chang YG / Ellisdon AM
History
DepositionAug 28, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72378.png

Downloads & links

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Map

FileDownload / File: emd_72378.map.gz / Format: CCP4 / Size: 9.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMReady sharpened focused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 137 pix.
= 137. Å		1 Å/pix.
x 137 pix.
= 137. Å		1 Å/pix.
x 137 pix.
= 137. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-0.41538668 - 14.676329000000001
Average (Standard dev.)0.41640976 (±1.4169925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions137137137
Spacing137137137
CellA=B=C: 137.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72378_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw unsharpened map (same as consensus)

Fileemd_72378_additional_1.map
AnnotationRaw unsharpened map (same as consensus)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_72378_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_72378_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KI...

EntireName: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
Components
  • Complex: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
    • Protein or peptide: GATOR1 complex protein DEPDC5

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Supramolecule #1: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KI...

SupramoleculeName: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: GATOR1 complex protein DEPDC5

MacromoleculeName: GATOR1 complex protein DEPDC5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 379.2355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDYKDDDDK GGGGGASTMR TTKVYKLVIH KKGFGGSDDE LVVNPKVFPH IKLGDIVEIA HPNDEYSPLL LQVKSLKEDL QKETISVDQ TVTQVFRLRP YQDVYVNVVD PKDVTLDLVE LTFKDQYIGR GDMWRLKKSL VSTCAYITQK VEFAGIRAQA G ELWVKNEK ...String:
MGDYKDDDDK GGGGGASTMR TTKVYKLVIH KKGFGGSDDE LVVNPKVFPH IKLGDIVEIA HPNDEYSPLL LQVKSLKEDL QKETISVDQ TVTQVFRLRP YQDVYVNVVD PKDVTLDLVE LTFKDQYIGR GDMWRLKKSL VSTCAYITQK VEFAGIRAQA G ELWVKNEK VMCGYISEDT RVVFRSTSAM VYIFIQMSCE MWDFDIYGDL YFEKAVNGFL ADLFTKWKEK NCSHEVTVVL FS RTFYDAK SVDEFPEINR ASIRQDHKGR FYEDFYKVVV QNERREEWTS LLVTIKKLFI QYPVLVRLEQ AEGFPQGDNS TSA QGNYLE AINLSFNVFD KHYINRNFDR TGQMSVVITP GVGVFEVDRL LMILTKQRMI DNGIGVDLVC MGEQPLHAVP LFKL HNRSA PRDSRLGDDY NIPHWINHSF YTSKSQLFCN SFTPRIKLAG KKPASEKAKN GRDTSLGSPK ESENALPIQV DYDAY DAQV FRLPGPSRAQ CLTTCRSVRE RESHSRKSAS SCDVSSSPSL PSRTLPTEEV RSQASDDSSL GKSANILMIP HPHLHQ YEV SSSLGYTSTR DVLENMMEPP QRDSSAPGRF HVGSAESMLH VRPGGYTPQR ALINPFAPSR MPMKLTSNRR RWMHTFP VG PSGEAIQIHH QTRQNMAELQ GSGQRDPTHS SAELLELAYH EAAGRHSNSR QPGDGMSFLN FSGTEELSVG LLSNSGAG M NPRTQNKDSL EDSVSTSPDP ILTLSAPPVV PGFCCTVGVD WKSLTTPACL PLTTDYFPDR QGLQNDYTEG CYDLLPEAD IDRRDEDGVQ MTAQQVFEEF ICQRLMQGYQ IIVQPKTQKP NPAVPPPLSS SPLYSRGLVS RNRPEEEDQY WLSMGRTFHK VTLKDKMIT VTRYLPKYPY ESAQIHYTYS LCPSHSDSEF VSCWVEFSHE RLEEYKWNYL DQYICSAGSE DFSLIESLKF W RTRFLLLP ACVTATKRIT EGEAHCDIYG DRPRADEDEW QLLDGFVRFV EGLNRIRRRH RSDRMMRKGT AMKGLQMTGP IS THSLEST APPVGKKGTS ALSALLEMEA SQKCLGEQQA AVHGGKSSAQ SAESSSVAMT PTYMDSPRKD GAFFMEFVRS PRT ASSAFY PQVSVDQTAT PMLDGTSLGI CTGQSMDRGN SQTFGNSQNI GEQGYSSTNS SDSSSQQLVA SSLTSSSTLT EILE AMKHP STGVQLLSEQ KGLSPYCFIS AEVVHWLVNH VEGIQTQAMA IDIMQKMLEE QLITHASGEA WRTFIYGFYF YKIVT DKEP DRVAMQQPAT TWHTAGVDDF ASFQRKWFEV AFVAEELVHS EIPAFLLPWL PSRPASYASR HSSFSRSFGG RSQAAA LLA ATVPEQRTVT LDVDVNNRTD RLEWCSCYYH GNFSLNAAFE IKLHWMAVTA AVLFEMVQGW HRKATSCGFL LVPVLEG PF ALPSYLYGDP LRAQLFIPLN ISCLLKEGSE HLFDSFEPET YWDRMHLFQE AIAHRFGFVQ DKYSASAFNF PAENKPQY I HVTGTVFLQL PYSKRKFSGQ QRRRRNSTSS TNQNMFCEER VGYNWAYNTM LTKTWRSSAT GDEKFADRLL KDFTDFCIN RDNRLVTFWT SCLEKMHASA PGGASGSYYR AEKGQGSGAE PQSGHSSRGS GSFVKFFTYS TQPTGSGGGM ASMGHTGLKG GSGGDSQCG TSMSGQESGQ GGGGGQGGDG GVGLSGIGGG AGATDSGIPG LGVSGGENGG KASPGGTPAP KMMTTQSTCG F NGGSTGLG GTGSGQMGKG RSTMRTTKVY KLVIHKKGFG GSDDELVVNP KVFPHIKLGD IVEIAHPNDE YSPLLLQVKS LK EDLQKET ISVDQTVTQV FRLRPYQDVY VNVVDPKDVT LDLVELTFKD QYIGRGDMWR LKKSLVSTCA YITQKVEFAG IRA QAGELW VKNEKVMCGY ISEDTRVVFR STSAMVYIFI QMSCEMWDFD IYGDLYFEKA VNGFLADLFT KWKEKNCSHE VTVV LFSRT FYDAKSVDEF PEINRASIRQ DHKGRFYEDF YKVVVQNERR EEWTSLLVTI KKLFIQYPVL VRLEQAEGFP QGDNS TSAQ GNYLEAINLS FNVFDKHYIN RNFDRTGQMS VVITPGVGVF EVDRLLMILT KQRMIDNGIG VDLVCMGEQP LHAVPL FKL HNRSAPRDSR LGDDYNIPHW INHSFYTSKS QLFCNSFTPR IKLAGKKPAS EKAKNGRDTS LGSPKESENA LPIQVDY DA YDAQVFRLPG PSRAQCLTTC RSVRERESHS RKSASSCDVS SSPSLPSRTL PTEEVRSQAS DDSSLGKSAN ILMIPHPH L HQYEVSSSLG YTSTRDVLEN MMEPPQRDSS APGRFHVGSA ESMLHVRPGG YTPQRALINP FAPSRMPMKL TSNRRRWMH TFPVGPSGEA IQIHHQTRQN MAELQGSGQR DPTHSSAELL ELAYHEAAGR HSNSRQPGDG MSFLNFSGTE ELSVGLLSNS GAGMNPRTQ NKDSLEDSVS TSPDPILTLS APPVVPGFCC TVGVDWKSLT TPACLPLTTD YFPDRQGLQN DYTEGCYDLL P EADIDRRD EDGVQMTAQQ VFEEFICQRL MQGYQIIVQP KTQKPNPAVP PPLSSSPLYS RGLVSRNRPE EEDQYWLSMG RT FHKVTLK DKMITVTRYL PKYPYESAQI HYTYSLCPSH SDSEFVSCWV EFSHERLEEY KWNYLDQYIC SAGSEDFSLI ESL KFWRTR FLLLPACVTA TKRITEGEAH CDIYGDRPRA DEDEWQLLDG FVRFVEGLNR IRRRHRSDRM MRKGTAMKGL QMTG PISTH SLESTAPPVG KKGTSALSAL LEMEASQKCL GEQQAAVHGG KSSAQSAESS SVAMTPTYMD SPRKDGAFFM EFVRS PRTA SSAFYPQVSV DQTATPMLDG TSLGICTGQS MDRGNSQTFG NSQNIGEQGY SSTNSSDSSS QQLVASSLTS SSTLTE ILE AMKHPSTGVQ LLSEQKGLSP YCFISAEVVH WLVNHVEGIQ TQAMAIDIMQ KMLEEQLITH ASGEAWRTFI YGFYFYK IV TDKEPDRVAM QQPATTWHTA GVDDFASFQR KWFEVAFVAE ELVHSEIPAF LLPWLPSRPA SYASRHSSFS RSFGGRSQ A AALLAATVPE QRTVTLDVDV NNRTDRLEWC SCYYHGNFSL NAAFEIKLHW MAVTAAVLFE MVQGWHRKAT SCGFLLVPV LEGPFALPSY LYGDPLRAQL FIPLNISCLL KEGSEHLFDS FEPETYWDRM HLFQEAIAHR FGFVQDKYSA SAFNFPAENK PQYIHVTGT VFLQLPYSKR KFSGQQRRRR NSTSSTNQNM FCEERVGYNW AYNTMLTKTW RSSATGDEKF ADRLLKDFTD F CINRDNRL VTFWTSCLEK MHASAP

UniProtKB: GATOR1 complex protein DEPDC5

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 356922
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 28288
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Software - details: SpIsoNet refinement
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9o5e


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9xzy:
DEPDC5 dimer (tandem DEPDC5) focused map

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