+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40669 | |||||||||
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Title | Structure of human PI3KC3-C1 complex | |||||||||
Map data | Composite map | |||||||||
Sample |
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Keywords | Autophagy / Lipid kinase / Complex / 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 / phosphatidylinositol 3-kinase complex, class III ...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 / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / mitochondria-associated endoplasmic reticulum membrane contact site / 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 / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / engulfment of apoptotic cell / regulation of protein complex stability / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / phagophore assembly site membrane / suppression by virus of host autophagy / protein targeting to lysosome / protein targeting to vacuole / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / SMAD protein signal transduction / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / post-transcriptional regulation of gene expression / mitotic metaphase chromosome alignment / Macroautophagy / cytoplasmic pattern recognition receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / autophagosome membrane docking / lysosome organization / RSV-host interactions / endosome to lysosome transport / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / axoneme / autophagosome membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / mitophagy / autophagosome maturation / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / response to vitamin E / autophagosome / neuron development / negative regulation of reactive oxygen species metabolic process / regulation of macroautophagy / amyloid-beta metabolic process / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / cellular response to starvation / phagocytic vesicle / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein phosphorylation / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / regulation of protein phosphorylation / trans-Golgi network / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / endocytosis / phagocytic vesicle membrane / peroxisome / microtubule cytoskeleton / late endosome / GTPase binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 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_40669.map.gz | 167.8 MB | EMDB map data format | |
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Header (meta data) | emd-40669-v30.xml emd-40669.xml | 26.8 KB 26.8 KB | Display Display | EMDB header |
Images | emd_40669.png | 86.7 KB | ||
Others | emd_40669_additional_1.map.gz emd_40669_additional_2.map.gz emd_40669_additional_3.map.gz | 168 MB 164.7 MB 164.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40669 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40669 | HTTPS FTP |
-Validation report
Summary document | emd_40669_validation.pdf.gz | 502.4 KB | Display | EMDB validaton report |
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Full document | emd_40669_full_validation.pdf.gz | 502 KB | Display | |
Data in XML | emd_40669_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_40669_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40669 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40669 | HTTPS FTP |
-Related structure data
Related structure data | 8sorMC 8soiC 8sqzC 8srmC 8srqC C: citing same article (ref.) M: atomic model generated by this map |
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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_40669.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.115 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Consensus map
File | emd_40669_additional_1.map | ||||||||||||
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Annotation | Consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refinement map 1/2
File | emd_40669_additional_2.map | ||||||||||||
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Annotation | Local refinement map 1/2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refinement map 2/2
File | emd_40669_additional_3.map | ||||||||||||
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Annotation | Local refinement map 2/2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human autophagy initiation PI3KC3-C1 complex
Entire | Name: Human autophagy initiation PI3KC3-C1 complex |
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Components |
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-Supramolecule #1: Human autophagy initiation PI3KC3-C1 complex
Supramolecule | Name: Human autophagy initiation PI3KC3-C1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 362 KDa |
-Macromolecule #1: Phosphatidylinositol 3-kinase catalytic subunit type 3
Macromolecule | Name: Phosphatidylinositol 3-kinase catalytic subunit type 3 type: protein_or_peptide / ID: 1 / 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 |
-Macromolecule #2: Beclin 1-associated autophagy-related key regulator
Macromolecule | Name: Beclin 1-associated autophagy-related key regulator / type: protein_or_peptide / ID: 2 / 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 |
-Macromolecule #3: Beclin-1
Macromolecule | Name: Beclin-1 / 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: 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 |
-Macromolecule #4: Phosphoinositide 3-kinase regulatory subunit 4
Macromolecule | Name: Phosphoinositide 3-kinase regulatory subunit 4 / type: protein_or_peptide / ID: 4 / 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 |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / 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 |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2243 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / 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: 36000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-8sor: |