+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45297 | |||||||||
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Title | Structure of human ULK1C:PI3KC3-C1 supercomplex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Autophagy / Protein kinase / Lipid kinase / Supercomplex / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / regulation of protein lipidation ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / regulation of protein lipidation / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / ribophagy / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of stress granule assembly / Atg1/ULK1 kinase complex / mitochondria-associated endoplasmic reticulum membrane contact site / autophagy of peroxisome / glycophagy / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / receptor catabolic process / positive regulation of autophagosome assembly / engulfment of apoptotic cell / phosphatidylinositol kinase activity / negative regulation of autophagosome assembly / regulation of protein complex stability / phosphatidylinositol 3-kinase regulator activity / protein targeting to vacuole / suppression by virus of host autophagy / protein localization to phagophore assembly site / protein targeting to lysosome / phagophore assembly site membrane / late endosome to vacuole transport / early endosome to late endosome transport / SMAD protein signal transduction / piecemeal microautophagy of the nucleus / negative regulation of programmed cell death / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / cytoplasmic pattern recognition receptor signaling pathway / autophagy of mitochondrion / response to iron(II) ion / cellular response to nitrogen starvation / reticulophagy / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / autophagosome membrane docking / mitotic metaphase chromosome alignment / post-transcriptional regulation of gene expression / 1-phosphatidylinositol-3-kinase activity / endosome to lysosome transport / lysosome organization / Macroautophagy / RSV-host interactions / positive regulation of cardiac muscle hypertrophy / autolysosome / p38MAPK cascade / phosphatidylinositol-mediated signaling / axoneme / phosphatidylinositol phosphate biosynthetic process / autophagosome membrane / PI3K Cascade / positive regulation of cell size / autophagosome maturation / neuron development / autophagosome assembly / mitophagy / RHO GTPases Activate NADPH Oxidases / response to vitamin E / negative regulation of reactive oxygen species metabolic process / amyloid-beta metabolic process / regulation of macroautophagy / cellular defense response / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / phagocytic vesicle / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of autophagy / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / JNK cascade / cellular response to copper ion / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / autophagosome / cellular response to starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein phosphorylation / liver development / regulation of cytokinesis / regulation of autophagy / negative regulation of extrinsic apoptotic signaling pathway / macroautophagy Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.84 Å | |||||||||
Authors | Chen M / Hurley JH | |||||||||
Funding support | United States, 2 items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex Authors: Chen M / Ren X / Cook A / Hurley JH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45297.map.gz | 631.8 MB | EMDB map data format | |
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Header (meta data) | emd-45297-v30.xml emd-45297.xml | 27.3 KB 27.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45297_fsc.xml | 18.8 KB | Display | FSC data file |
Images | emd_45297.png | 52.6 KB | ||
Filedesc metadata | emd-45297.cif.gz | 8.8 KB | ||
Others | emd_45297_additional_1.map.gz emd_45297_half_map_1.map.gz emd_45297_half_map_2.map.gz | 631.9 MB 621.8 MB 621.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45297 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45297 | HTTPS FTP |
-Validation report
Summary document | emd_45297_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_45297_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_45297_validation.xml.gz | 28 KB | Display | |
Data in CIF | emd_45297_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45297 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45297 | HTTPS FTP |
-Related structure data
Related structure data | 9c82MC 8soiC 8sorC 8sqzC 8srmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_45297.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_45297_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_45297_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_45297_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
Entire | Name: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex |
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Components |
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-Supramolecule #1: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
Supramolecule | Name: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Individually expressed the ULK1 complex core (consists of two molecules of FIP200 (1-640), ULK1 (828-1050), and ATG13 (363-517)) and the full-length PI3KC3-C1 (consists of VPS34, VPS15, ...Details: Individually expressed the ULK1 complex core (consists of two molecules of FIP200 (1-640), ULK1 (828-1050), and ATG13 (363-517)) and the full-length PI3KC3-C1 (consists of VPS34, VPS15, BECN1, and ATG14). Mixed the above two complexes in a molecular ratio of 1.5:1 and purified the supercomplex by strep pulldown of the TSF-tagged VPS15. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 550 KDa |
-Macromolecule #1: Phosphoinositide 3-kinase regulatory subunit 4
Macromolecule | Name: Phosphoinositide 3-kinase regulatory subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 153.293797 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP TLPLTSYKQE LEELKIRLNS AQNCLPFQK ASEKASEKAA MLFRQYVRDN LYDRISTRPF LNNIEKRWIA FQILTAVDQA HKSGVRHGDI KTENVMVTSW N WVLLTDFA ...String: MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP TLPLTSYKQE LEELKIRLNS AQNCLPFQK ASEKASEKAA MLFRQYVRDN LYDRISTRPF LNNIEKRWIA FQILTAVDQA HKSGVRHGDI KTENVMVTSW N WVLLTDFA SFKPTYLPED NPADFNYFFD TSRRRTCYIA PERFVDGGMF ATELEYMRDP STPLVDLNSN QRTRGELKRA MD IFSAGCV IAELFTEGVP LFDLSQLLAY RNGHFFPEQV LNKIEDHSIR ELVTQMIHRE PDKRLEAEDY LKQQRGNAFP EIF YTFLQP YMAQFAKETF LSADERILVI RKDLGNIIHN LCGHDLPEKA EGEPKENGLV ILVSVITSCL QTLKYCDSKL AALE LILHL APRLSVEILL DRITPYLLHF SNDSVPRVRA EALRTLTKVL ALVKEVPRND INIYPEYILP GIAHLAQDDA TIVRL AYAE NIALLAETAL RFLELVQLKN LNMENDPNNE EIDEVTHPNG NYDTELQALH EMVQQKVVTL LSDPENIVKQ TLMENG ITR LCVFFGRQKA NDVLLSHMIT FLNDKNDWHL RGAFFDSIVG VAAYVGWQSS SILKPLLQQG LSDAEEFVIV KALYALT CM CQLGLLQKPH VYEFASDIAP FLCHPNLWIR YGAVGFITVV ARQISTADVY CKLMPYLDPY ITQPIIQIER KLVLLSVL K EPVSRSIFDY ALRSKDITSL FRHLHMRQKK RNGSLPDCPP PEDPAIAQLL KKLLSQGMTE EEEDKLLALK DFMMKSNKA KANIVDQSHL HDSSQKGVID LAALGITGRQ VDLVKTKQEP DDKRARKHVK QDSNVNEEWK SMFGSLDPPN MPQALPKGSD QEVIQTGKP PRSESSAGIC VPLSTSSQVP EVTTVQNKKP VIPVLSSTIL PSTYQIRITT CKTELQQLIQ QKREQCNAER I AKQMMENA EWESKPPPPG WRPKGLLVAH LHEHKSAVNR IRVSDEHSLF ATCSNDGTVK IWNSQKMEGK TTTTRSILTY SR IGGRVKT LTFCQGSHYL AIASDNGAVQ LLGIEASKLP KSPKIHPLQS RILDQKEDGC VVDMHHFNSG AQSVLAYATV NGS LVGWDL RSSSNAWTLK HDLKSGLITS FAVDIHQCWL CIGTSSGTMA CWDMRFQLPI SSHCHPSRAR IRRLSMHPLY QSWV IAAVQ GNNEVSMWDM ETGDRRFTLW ASSAPPLSEL QPSPHSVHGI YCSPADGNPI LLTAGSDMKI RFWDLAYPER SYVVA GSTS SPSVSYYRKI IEGTEVVQEI QNKQKVGPSD DTPRRGPESL PVGHHDIITD VATFQTTQGF IVTASRDGIV KVWK UniProtKB: Phosphoinositide 3-kinase regulatory subunit 4 |
-Macromolecule #2: Phosphatidylinositol 3-kinase catalytic subunit type 3
Macromolecule | Name: Phosphatidylinositol 3-kinase catalytic subunit type 3 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphatidylinositol 3-kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 101.680328 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGEAEKFHYI YSCDLDINVQ LKIGSLEGKR EQKSYKAVLE DPMLKFSGLY QETCSDLYVT CQVFAEGKPL ALPVRTSYKA FSTRWNWNE WLKLPVKYPD LPRNAQVALT IWDVYGPGKA VPVGGTTVSL FGKYGMFRQG MHDLKVWPNV EADGSEPTKT P GRTSSTLS ...String: MGEAEKFHYI YSCDLDINVQ LKIGSLEGKR EQKSYKAVLE DPMLKFSGLY QETCSDLYVT CQVFAEGKPL ALPVRTSYKA FSTRWNWNE WLKLPVKYPD LPRNAQVALT IWDVYGPGKA VPVGGTTVSL FGKYGMFRQG MHDLKVWPNV EADGSEPTKT P GRTSSTLS EDQMSRLAKL TKAHRQGHMV KVDWLDRLTF REIEMINESE KRSSNFMYLM VEFRCVKCDD KEYGIVYYEK DG DESSPIL TSFELVKVPD PQMSMENLVE SKHHKLARSL RSGPSDHDLK PNAATRDQLN IIVSYPPTKQ LTYEEQDLVW KFR YYLTNQ EKALTKFLKC VNWDLPQEAK QALELLGKWK PMDVEDSLEL LSSHYTNPTV RRYAVARLRQ ADDEDLLMYL LQLV QALKY ENFDDIKNGL EPTKKDSQSS VSENVSNSGI NSAEIDSSQI ITSPLPSVSS PPPASKTKEV PDGENLEQDL CTFLI SRAC KNSTLANYLY WYVIVECEDQ DTQQRDPKTH EMYLNVMRRF SQALLKGDKS VRVMRSLLAA QQTFVDRLVH LMKAVQ RES GNRKKKNERL QALLGDNEKM NLSDVELIPL PLEPQVKIRG IIPETATLFK SALMPAQLFF KTEDGGKYPV IFKHGDD LR QDQLILQIIS LMDKLLRKEN LDLKLTPYKV LATSTKHGFM QFIQSVPVAE VLDTEGSIQN FFRKYAPSEN GPNGISAE V MDTYVKSCAG YCVITYILGV GDRHLDNLLL TKTGKLFHID FGYILGRDPK PLPPPMKLNK EMVEGMGGTQ SEQYQEFRK QCYTAFLHLR RYSNLILNLF SLMVDANIPD IALEPDKTVK KVQDKFRLDL SDEEAVHYMQ SLIDESVHAL FAAVVEQIHK FAQYWRK UniProtKB: Phosphatidylinositol 3-kinase catalytic subunit type 3 |
-Macromolecule #3: Beclin 1-associated autophagy-related key regulator
Macromolecule | Name: Beclin 1-associated autophagy-related key regulator / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.387266 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASPSGKGAR ALEAPGCGPR PLARDLVDSV DDAEGLYVAV ERCPLCNTTR RRLTCAKCVQ SGDFVYFDGR DRERFIDKKE RLSRLKSKQ EEFQKEVLKA MEGKWITDQL RWKIMSCKMR IEQLKQTICK GNEEMEKNSE GLLKTKEKNQ KLYSRAQRHQ E KKEKIQRH ...String: MASPSGKGAR ALEAPGCGPR PLARDLVDSV DDAEGLYVAV ERCPLCNTTR RRLTCAKCVQ SGDFVYFDGR DRERFIDKKE RLSRLKSKQ EEFQKEVLKA MEGKWITDQL RWKIMSCKMR IEQLKQTICK GNEEMEKNSE GLLKTKEKNQ KLYSRAQRHQ E KKEKIQRH NRKLGDLVEK KTIDLRSHYE RLANLRRSHI LELTSVIFPI EEVKTGVRDP ADVSSESDSA MTSSTVSKLA EA RRTTYLS GRWVCDDHNG DTSISITGPW ISLPNNGDYS AYYSWVEEKK TTQGPDMEQS NPAYTISAAL CYATQLVNIL SHI LDVNLP KKLCNSEFCG ENLSKQKFTR AVKKLNANIL YLCFSQHVNL DQLQPLHTLR NLMYLVSPSS EHLGRSGPFE VRAD LEESM EFVDPGVAGE SDESGDERVS DEETDLGTDW ENLPSPRFCD IPSQSVEVSQ SQSTQASPPI ASSSAGGMIS SAAAS VTSW FKAYTGHR UniProtKB: Beclin 1-associated autophagy-related key regulator |
-Macromolecule #4: Beclin-1
Macromolecule | Name: Beclin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 51.953102 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEGSKTSNNS TMQVSFVCQR CSQPLKLDTS FKILDRVTIQ ELTAPLLTTA QAKPGETQEE ETNSGEEPFI ETPRQDGVSR RFIPPARMM STESANSFTL IGEASDGGTM ENLSRRLKVT GDLFDIMSGQ TDVDHPLCEE CTDTLLDQLD TQLNVTENEC Q NYKRCLEI ...String: MEGSKTSNNS TMQVSFVCQR CSQPLKLDTS FKILDRVTIQ ELTAPLLTTA QAKPGETQEE ETNSGEEPFI ETPRQDGVSR RFIPPARMM STESANSFTL IGEASDGGTM ENLSRRLKVT GDLFDIMSGQ TDVDHPLCEE CTDTLLDQLD TQLNVTENEC Q NYKRCLEI LEQMNEDDSE QLQMELKELA LEEERLIQEL EDVEKNRKIV AENLEKVQAE AERLDQEEAQ YQREYSEFKR QQ LELDDEL KSVENQMRYA QTQLDKLKKT NVFNATFHIW HSGQFGTINN FRLGRLPSVP VEWNEINAAW GQTVLLLHAL ANK MGLKFQ RYRLVPYGNH SYLESLTDKS KELPLYCSGG LRFFWDNKFD HAMVAFLDCV QQFKEEVEKG ETRFCLPYRM DVEK GKIED TGGSGGSYSI KTQFNSEEQW TKALKFMLTN LKWGLAWVSS QFYNK UniProtKB: Beclin-1 |
-Macromolecule #5: RB1-inducible coiled-coil protein 1
Macromolecule | Name: RB1-inducible coiled-coil protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73.325633 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKLYVFLVNT GTTLTFDTEL TVQTVADLKH AIQSKYKIAI QHQVLVVNGG ECMAADRRVC TYSAGTDTNP IFLFNKEMIL CDRPPAIPK TTFSTENDME IKVEESLMMP AVFHTVASRT QLALEMYEVA KKLCSFCEGL VHDEHLQHQG WAAIMANLED C SNSYQKLL ...String: MKLYVFLVNT GTTLTFDTEL TVQTVADLKH AIQSKYKIAI QHQVLVVNGG ECMAADRRVC TYSAGTDTNP IFLFNKEMIL CDRPPAIPK TTFSTENDME IKVEESLMMP AVFHTVASRT QLALEMYEVA KKLCSFCEGL VHDEHLQHQG WAAIMANLED C SNSYQKLL FKFESIYSNY LQSIEDIKLK LTHLGTAVSV MAKIPLLECL TRHSYRECLG RLDSLPEHED SEKAEMKRST EL VLSPDMP RTTNESLLTS FPKSVEHVSP DTADAESGKE IRESCQSTVH QQDETTIDTK DGDLPFFNVS LLDWINVQDR PND VESLVR KCFDSMSRLD PRIIRPFIAE CRQTIAKLDN QNMKAIKGLE DRLYALDQMI ASCGRLVNEQ KELAQGFLAN QKRA ENLKD ASVLPDLCLS HANQLMIMLQ NHRKLLDIKQ KCTTAKQELA NNLHVRLKWC CFVMLHADQD GEKLQALLRL VIELL ERVK IVEALSTVPQ MYCLAVVEVV RRKMFIKHYR EWAGALVKDG KRLYEAEKSK RESFGKLFRK SFLRNRLFRG LDSWPP SFC TQKPRKFDCE LPDISLKDLQ FLQSFCPSEV QPFLRVPLLC DFEPLHQHVL ALHNLVKAAQ SLDEMSQTIT DLLSEQK UniProtKB: RB1-inducible coiled-coil protein 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: added 0.05% (w/v) octylglucopyranoside as surfactant. | ||||||||||||||||||
Details | This sample was purified by strep pulldown. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-9c82: |