+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7464 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of GATOR1-RAG | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | mTORC1 amino-acid sensing lysosome growth control / SIGNALING PROTEIN | ||||||||||||||||||||||||
Function / homology | Function and homology information GATOR1 complex / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / aorta morphogenesis / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 ...GATOR1 complex / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / aorta morphogenesis / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / cardiac muscle tissue development / enzyme-substrate adaptor activity / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / small GTPase-mediated signal transduction / Macroautophagy / roof of mouth development / mTORC1-mediated signalling / positive regulation of TOR signaling / response to amino acid / cellular response to nutrient levels / positive regulation of autophagy / protein-membrane adaptor activity / negative regulation of TORC1 signaling / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / positive regulation of TORC1 signaling / cellular response to starvation / cellular response to amino acid starvation / GTPase activator activity / negative regulation of autophagy / cellular response to amino acid stimulus / RNA splicing / TP53 Regulates Metabolic Genes / phosphoprotein binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / small GTPase binding / GDP binding / protein localization / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / molecular adaptor activity / lysosome / intracellular signal transduction / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / DNA-templated transcription / ubiquitin protein ligase binding / protein-containing complex binding / GTP binding / apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||||||||||||||
Authors | Shen K / Huang RK / Brignole EJ / Yu Z / Sabatini DM | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Nature / Year: 2018 Title: Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Authors: Kuang Shen / Rick K Huang / Edward J Brignole / Kendall J Condon / Max L Valenstein / Lynne Chantranupong / Aimaiti Bomaliyamu / Abigail Choe / Chuan Hong / Zhiheng Yu / David M Sabatini / Abstract: Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase- ...Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7464.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-7464-v30.xml emd-7464.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_7464.png | 200.3 KB | ||
Filedesc metadata | emd-7464.cif.gz | 7.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7464 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7464 | HTTPS FTP |
-Validation report
Summary document | emd_7464_validation.pdf.gz | 382.6 KB | Display | EMDB validaton report |
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Full document | emd_7464_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | emd_7464_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | emd_7464_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7464 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7464 | HTTPS FTP |
-Related structure data
Related structure data | 6cesMC 7465C 6cetC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7464.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GATOR1-RAG
Entire | Name: GATOR1-RAG |
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Components |
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-Supramolecule #1: GATOR1-RAG
Supramolecule | Name: GATOR1-RAG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 370 KDa |
-Macromolecule #1: GATOR complex protein NPRL2
Macromolecule | Name: GATOR complex protein NPRL2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 43.711395 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGSGCRIECI FFSEFHPTLG PKITYQVPED FISRELFDTV QVYIITKPEL QNKLITVTAM EKKLIGCPVC IEHKKYSRNA LLFNLGFVC DAQAKTCALE PIVKKLAGYL TTLELESSFV SMEESKQKLV PIMTILLEEL NASGRCTLPI DESNTIHLKV I EQRPDPPV ...String: MGSGCRIECI FFSEFHPTLG PKITYQVPED FISRELFDTV QVYIITKPEL QNKLITVTAM EKKLIGCPVC IEHKKYSRNA LLFNLGFVC DAQAKTCALE PIVKKLAGYL TTLELESSFV SMEESKQKLV PIMTILLEEL NASGRCTLPI DESNTIHLKV I EQRPDPPV AQEYDVPVFT KDKEDFFNSQ WDLTTQQILP YIDGFRHIQK ISAEADVELN LVRIAIQNLL YYGVVTLVSI LQ YSNVYCP TPKVQDLVDD KSLQEACLSY VTKQGHKRAS LRDVFQLYCS LSPGTTVRDL IGRHPQQLQH VDERKLIQFG LMK NLIRRL QKYPVRVTRE EQSHPARLYT GCHSYDEICC KTGMSYHELD ERLENDPNII ICWK UniProtKB: GATOR1 complex protein NPRL2 |
-Macromolecule #2: GATOR complex protein NPRL3
Macromolecule | Name: GATOR complex protein NPRL3 / 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: 63.68082 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MRDNTSPISV ILVSSGSRGN KLLFRYPFQR SQEHPASQTS KPRSRYAASN TGDHADEQDG DSRFSDVILA TILATKSEMC GQKFELKID NVRFVGHPTL LQHALGQISK TDPSPKREAP TMILFNVVFA LRANADPSVI NCLHNLSRRI ATVLQHEERR C QYLTREAK ...String: MRDNTSPISV ILVSSGSRGN KLLFRYPFQR SQEHPASQTS KPRSRYAASN TGDHADEQDG DSRFSDVILA TILATKSEMC GQKFELKID NVRFVGHPTL LQHALGQISK TDPSPKREAP TMILFNVVFA LRANADPSVI NCLHNLSRRI ATVLQHEERR C QYLTREAK LILALQDEVS AMADGNEGPQ SPFHHILPKC KLARDLKEAY DSLCTSGVVR LHINSWLEVS FCLPHKIHYA AS SLIPPEA IERSLKAIRP YHALLLLSDE KSLLGELPID CSPALVRVIK TTSAVKNLQQ LAQDADLALL QVFQLAAHLV YWG KAIIIY PLCENNVYML SPNASVCLYS PLAEQFSHQF PSHDLPSVLA KFSLPVSLSE FRNPLAPAVQ ETQLIQMVVW MLQR RLLIQ LHTYVCLMAS PSEEEPRPRE DDVPFTARVG GRSLSTPNAL SFGSPTSSDD MTLTSPSMDN SSAELLPSGD SPLNQ RMTE NLLASLSEHE RAAILSVPAA QNPEDLRMFA RLLHYFRGRH HLEEIMYNEN TRRSQLLMLF DKFRSVLVVT THEDPV IAV FQALLP UniProtKB: GATOR1 complex protein NPRL3 |
-Macromolecule #3: GATOR complex protein DEPDC5
Macromolecule | Name: GATOR complex protein DEPDC5 / 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: 181.478 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MRTTKVYKLV IHKKGFGGSD DELVVNPKVF PHIKLGDIVE IAHPNDEYSP LLLQVKSLKE DLQKETISVD QTVTQVFRLR PYQDVYVNV VDPKDVTLDL VELTFKDQYI GRGDMWRLKK SLVSTCAYIT QKVEFAGIRA QAGELWVKNE KVMCGYISED T RVVFRSTS ...String: MRTTKVYKLV IHKKGFGGSD DELVVNPKVF PHIKLGDIVE IAHPNDEYSP LLLQVKSLKE DLQKETISVD QTVTQVFRLR PYQDVYVNV VDPKDVTLDL VELTFKDQYI GRGDMWRLKK SLVSTCAYIT QKVEFAGIRA QAGELWVKNE KVMCGYISED T RVVFRSTS AMVYIFIQMS CEMWDFDIYG DLYFEKAVNG FLADLFTKWK EKNCSHEVTV VLFSRTFYDA KSVDEFPEIN RA SIRQDHK GRFYEDFYKV VVQNERREEW TSLLVTIKKL FIQYPVLVRL EQAEGFPQGD NSTSAQGNYL EAINLSFNVF DKH YINRNF DRTGQMSVVI TPGVGVFEVD RLLMILTKQR MIDNGIGVDL VCMGEQPLHA VPLFKLHNRS APRDSRLGDD YNIP HWINH SFYTSKSQLF CNSFTPRIKL AGKKPASEKA KNGRDTSLGS PKESENALPI QVDYDAYDAQ VFRLPGPSRA QCLTT CRSV RERESHSRKS ASSCDVSSSP SLPSRTLPTE EVRSQASDDS SLGKSANILM IPHPHLHQYE VSSSLGYTST RDVLEN MME PPQRDSSAPG RFHVGSAESM LHVRPGGYTP QRALINPFAP SRMPMKLTSN RRRWMHTFPV GPSGEAIQIH HQTRQNM AE LQGSGQRDPT HSSAELLELA YHEAAGRHSN SRQPGDGMSF LNFSGTEELS VGLLSNSGAG MNPRTQNKDS LEDSVSTS P DPILTLSAPP VVPGFCCTVG VDWKSLTTPA CLPLTTDYFP DRQGLQNDYT EGCYDLLPEA DIDRRDEDGV QMTAQQVFE EFICQRLMQG YQIIVQPKTQ KPNPAVPPPL SSSPLYSRGL VSRNRPEEED QYWLSMGRTF HKVTLKDKMI TVTRYLPKYP YESAQIHYT YSLCPSHSDS EFVSCWVEFS HERLEEYKWN YLDQYICSAG SEDFSLIESL KFWRTRFLLL PACVTATKRI T EGEAHCDI YGDRPRADED EWQLLDGFVR FVEGLNRIRR RHRSDRMMRK GTAMKGLQMT GPISTHSLES TAPPVGKKGT SA LSALLEM EASQKCLGEQ QAAVHGGKSS AQSAESSSVA MTPTYMDSPR KDGAFFMEFV RSPRTASSAF YPQVSVDQTA TPM LDGTSL GICTGQSMDR GNSQTFGNSQ NIGEQGYSST NSSDSSSQQL VASSLTSSST LTEILEAMKH PSTGVQLLSE QKGL SPYCF ISAEVVHWLV NHVEGIQTQA MAIDIMQKML EEQLITHASG EAWRTFIYGF YFYKIVTDKE PDRVAMQQPA TTWHT AGVD DFASFQRKWF EVAFVAEELV HSEIPAFLLP WLPSRPASYA SRHSSFSRSF GGRSQAAALL AATVPEQRTV TLDVDV NNR TDRLEWCSCY YHGNFSLNAA FEIKLHWMAV TAAVLFEMVQ GWHRKATSCG FLLVPVLEGP FALPSYLYGD PLRAQLF IP LNISCLLKEG SEHLFDSFEP ETYWDRMHLF QEAIAHRFGF VQDKYSASAF NFPAENKPQY IHVTGTVFLQ LPYSKRKF S GQQRRRRNST SSTNQNMFCE ERVGYNWAYN TMLTKTWRSS ATGDEKFADR LLKDFTDFCI NRDNRLVTFW TSCLEKMHA SAP UniProtKB: GATOR1 complex protein DEPDC5 |
-Macromolecule #4: Ras-related GTP-binding protein A
Macromolecule | Name: Ras-related GTP-binding protein A / 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: 36.615168 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPNTAMKKKV LLMGKSGSGK TSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGQDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET ...String: MPNTAMKKKV LLMGKSGSGK TSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGQDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET LYKAWSSIVY QLIPNVQQLE MNLRNFAQII EADEVLLFER ATFLVISHYQ CKEQRDVHRF EKISNIIKQF KL SCSKLAA SFQSMEVRNS NFAAFIDIFT SNTYVMVVMS DPSIPSAATL INIRNARKHF EKLERVDGPK HSLLMR UniProtKB: Ras-related GTP-binding protein A |
-Macromolecule #5: Ras-related GTP-binding protein C
Macromolecule | Name: Ras-related GTP-binding protein C / 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: 44.298859 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKNSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN ...String: MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKNSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN PDMNFEVFIH KVDGLSDDHK IETQRDIHQR ANDDLADAGL EKLHLSFYLT SIYDHSIFEA FSKVVQKLIP QL PTLENLL NIFISNSGIE KAFLFDVVSK IYIATDSSPV DMQSYELCCD MIDVVIDVSC IYGLKEDGSG SAYDKESMAI IKL NNTTVL YLKEVTKFLA LVCILREESF ERKGLIDYNF HCFRKAIHEV FEVGVTSHRS CGHQTSASSL KALTHNGTPR NAI UniProtKB: Ras-related GTP-binding protein C |
-Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: GNP |
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Molecular weight | Theoretical: 522.196 Da |
Chemical component information | ChemComp-GNP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Ab initio using EMAN2 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128533 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |