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- EMDB-70833: GATOR2 complex bound to arginine sensor CASTOR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-70833
TitleGATOR2 complex bound to arginine sensor CASTOR1
Map data
Sample
  • Complex: GATOR2 complex bound to arginine sensor CASTOR1
    • Complex: GATOR2 Complex
      • Protein or peptide: GATOR complex protein WDR24
      • Protein or peptide: GATOR complex protein WDR59
      • Protein or peptide: Nucleoporin SEH1
      • Protein or peptide: Protein SEC13 homolog
      • Protein or peptide: GATOR2 complex protein MIOS
    • Complex: CASTOR1
      • Protein or peptide: Cytosolic arginine sensor for mTORC1 subunit 1
  • Ligand: ZINC ION
KeywordsComplex / mTORC1 / Signaling / Nutrients / Amino Acid Sensing / SIGNALING PROTEIN
Function / homology
Function and homology information


oligodendrocyte progenitor proliferation / GATOR2 complex / cellular response to L-arginine / molecular sensor activity / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / central nervous system myelin formation / COPII-coated vesicle cargo loading / nuclear pore outer ring ...oligodendrocyte progenitor proliferation / GATOR2 complex / cellular response to L-arginine / molecular sensor activity / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / central nervous system myelin formation / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / protein K6-linked ubiquitination / attachment of mitotic spindle microtubules to kinetochore / Amino acids regulate mTORC1 / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / arginine binding / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / vacuolar membrane / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / oligodendrocyte differentiation / SUMOylation of DNA replication proteins / positive regulation of macroautophagy / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / mRNA transport / nuclear pore / cellular response to nutrient levels / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of TORC1 signaling / signaling adaptor activity / Mitotic Prometaphase / positive regulation of TORC1 signaling / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / protein sequestering activity / Resolution of Sister Chromatid Cohesion / cellular response to amino acid starvation / SUMOylation of chromatin organization proteins / HCMV Late Events / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / RHO GTPases Activate Formins / ER to Golgi transport vesicle membrane / Transcriptional regulation by small RNAs / RING-type E3 ubiquitin transferase / kinetochore / ISG15 antiviral mechanism / autophagy / protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / ubiquitin protein ligase activity / cell junction / nuclear envelope / protein transport / snRNP Assembly / defense response to Gram-positive bacterium / regulation of autophagy / lysosomal membrane / cell division / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
WDR59, modified RING finger, H2 subclass (C3H3C2-type) / MIOS, WD40 repeat / CASTOR family / CASTOR1, N-terminal / : / Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain / Cytosolic arginine sensor for mTORC1 subunit 1/2, ACT-like / : / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 ...WDR59, modified RING finger, H2 subclass (C3H3C2-type) / MIOS, WD40 repeat / CASTOR family / CASTOR1, N-terminal / : / Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain / Cytosolic arginine sensor for mTORC1 subunit 1/2, ACT-like / : / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid / CASTOR, ACT domain / : / : / RING/Ubox like zinc-binding domain / ACT domain / RWD domain profile. / RWD / RWD domain / Sec13/Seh1 family / ACT-like domain / Ubiquitin-conjugating enzyme/RWD-like / WD domain, G-beta repeat / 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
Similarity search - Domain/homology
Protein SEC13 homolog / GATOR2 complex protein WDR59 / Cytosolic arginine sensor for mTORC1 subunit 1 / Nucleoporin SEH1 / GATOR2 complex protein WDR24 / GATOR2 complex protein MIOS
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJansen RM / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA285366 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for mTORC1 regulation by the CASTOR1-GATOR2 complex.
Authors: Rachel M Jansen / Clément Maghe / Karla Tapia / Selina Wu / Serim Yang / Xuefeng Ren / Roberto Zoncu / James H Hurley /
Abstract: Mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-responsive master regulator of metabolism. Amino acids control the recruitment and activation of mTORC1 at the lysosome through the ...Mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-responsive master regulator of metabolism. Amino acids control the recruitment and activation of mTORC1 at the lysosome through the nucleotide loading state of the heterodimeric Rag GTPases. Under low nutrients, including arginine, the GTPase-activating protein complex GATOR1 promotes GTP hydrolysis on RagA/B, inactivating mTORC1. GATOR1 is regulated by the cage-like GATOR2 complex and cytosolic amino acid sensors. To understand how the arginine sensor CASTOR1 binds to GATOR2 to disinhibit GATOR1 under low cytosolic arginine, we determined the cryo-electron microscopy structure of human GATOR2 bound to CASTOR1 in the absence of arginine. Two MIOS WD40 domain β-propellers of the GATOR2 cage engage with both subunits of a single CASTOR1 homodimer. Each propeller binds to a negatively charged MIOS-binding interface on CASTOR1 that is distal to the arginine pocket. The structure shows how arginine-triggered loop ordering in CASTOR1 blocks the MIOS-binding interface, switches off its binding to GATOR2 and, thus, communicates to downstream mTORC1 activation.
History
DepositionMay 27, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70833.png

Downloads & links

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Map

FileDownload / File: emd_70833.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 560 pix.
= 588. Å		1.05 Å/pix.
x 560 pix.
= 588. Å		1.05 Å/pix.
x 560 pix.
= 588. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-0.03876651 - 2.2034242
Average (Standard dev.)0.02010157 (±0.034966033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GATOR2 complex bound to arginine sensor CASTOR1

EntireName: GATOR2 complex bound to arginine sensor CASTOR1
Components
  • Complex: GATOR2 complex bound to arginine sensor CASTOR1
    • Complex: GATOR2 Complex
      • Protein or peptide: GATOR complex protein WDR24
      • Protein or peptide: GATOR complex protein WDR59
      • Protein or peptide: Nucleoporin SEH1
      • Protein or peptide: Protein SEC13 homolog
      • Protein or peptide: GATOR2 complex protein MIOS
    • Complex: CASTOR1
      • Protein or peptide: Cytosolic arginine sensor for mTORC1 subunit 1
  • Ligand: ZINC ION

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Supramolecule #1: GATOR2 complex bound to arginine sensor CASTOR1

SupramoleculeName: GATOR2 complex bound to arginine sensor CASTOR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: GATOR2 Complex

SupramoleculeName: GATOR2 Complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#5, #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: CASTOR1

SupramoleculeName: CASTOR1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GATOR2 complex protein MIOS

MacromoleculeName: GATOR2 complex protein MIOS / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.700391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGTKPDILW APHHVDRFVV CDSELSLYHV ESTVNSELKA GSLRLSEDSA ATLLSINSDT PYMKCVAWYL NYDPECLLAV GQANGRVVL TSLGQDHNSK FKDLIGKEFV PKHARQCNTL AWNPLDSNWL AAGLDKHRAD FSVLIWDICS KYTPDIVPME K VKLSAGET ...String:
MSGTKPDILW APHHVDRFVV CDSELSLYHV ESTVNSELKA GSLRLSEDSA ATLLSINSDT PYMKCVAWYL NYDPECLLAV GQANGRVVL TSLGQDHNSK FKDLIGKEFV PKHARQCNTL AWNPLDSNWL AAGLDKHRAD FSVLIWDICS KYTPDIVPME K VKLSAGET ETTLLVTKPL YELGQNDACL SLCWLPRDQK LLLAGMHRNL AIFDLRNTSQ KMFVNTKAVQ GVTVDPYFHD RV ASFYEGQ VAIWDLRKFE KPVLTLTEQP KPLTKVAWCP TRTGLLATLT RDSNIIRLYD MQHTPTPIGD ETEPTIIERS VQP CDNYIA SFAWHPTSQN RMIVVTPNRT MSDFTVFERI SLAWSPITSL MWACGRHLYE CTEEENDNSL EKDIATKMRL RALS RYGLD TEQVWRNHIL AGNEDPQLKS LWYTLHFMKQ YTEDMDQKSP GNKGSLVYAG IKSIVKSSLG MVESSRHNWS GLDKQ SDIQ NLNEERILAL QLCGWIKKGT DVDVGPFLNS LVQEGEWERA AAVALFNLDI RRAIQILNEG ASSEKGDLNL NVVAMA LSG YTDEKNSLWR EMCSTLRLQL NNPYLCVMFA FLTSETGSYD GVLYENKVAV RDRVAFACKF LSDTQLNRYI EKLTNEM KE AGNLEGILLT GLTKDGVDLM ESYVDRTGDV QTASYCMLQG SPLDVLKDER VQYWIENYRN LLDAWRFWHK RAEFDIHR S KLDPSSKPLA QVFVSCNFCG KSISYSCSAV PHQGRGFSQY GVSGSPTKSK VTSCPGCRKP LPRCALCLIN MGTPVSSCP GGTKSDEKVD LSKDKKLAQF NNWFTWCHNC RHGGHAGHML SWFRDHAECP VSACTCKCMQ LDTTGNLVPA ETVQP

UniProtKB: GATOR2 complex protein MIOS

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Macromolecule #2: GATOR complex protein WDR24

MacromoleculeName: GATOR complex protein WDR24 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.326953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEKMSRVTTA LGGSVLTGRT MHCHLDAPAN AISVCRDAAQ VVVAGRSIFK IYAIEEEQFV EKLNLRVGRK PSLNLSCADV VWHQMDENL LATAATNGVV VTWNLGRPSR NKQDQLFTEH KRTVNKVCFH PTEAHVLLSG SQDGFMKCFD LRRKDSVSTF S GQSESVRD ...String:
MEKMSRVTTA LGGSVLTGRT MHCHLDAPAN AISVCRDAAQ VVVAGRSIFK IYAIEEEQFV EKLNLRVGRK PSLNLSCADV VWHQMDENL LATAATNGVV VTWNLGRPSR NKQDQLFTEH KRTVNKVCFH PTEAHVLLSG SQDGFMKCFD LRRKDSVSTF S GQSESVRD VQFSIRDYFT FASTFENGNV QLWDIRRPDR CERMFTAHNG PVFCCDWHPE DRGWLATGGR DKMVKVWDMT TH RAKEMHC VQTIASVARV KWRPECRHHL ATCSMMVDHN IYVWDVRRPF VPAAMFEEHR DVTTGIAWRH PHDPSFLLSG SKD SSLCQH LFRDASQPVE RANPEGLCYG LFGDLAFAAK ESLVAAESGR KPYTGDRRHP IFFKRKLDPA EPFAGLASSA LSVF ETEPG GGGMRWFVDT AERYALAGRP LAELCDHNAK VARELGRNQV AQTWTMLRII YCSPGLVPTA NLNHSVGKGG SCGLP LMNS FNLKDMAPGL GSETRLDRSK GDARSDTVLL DSSATLITNE DNEETEGSDV PADYLLGDVE GEEDELYLLD PEHAHP EDP ECVLPQEAFP LRHEIVDTPP GPEHLQDKAD SPHVSGSEAD VASLAPVDSS FSLLSVSHAL YDSRLPPDFF GVLVRDM LH FYAEQGDVQM AVSVLIVLGE RVRKDIDEQT QEHWYTSYID LLQRFRLWNV SNEVVKLSTS RAVSCLNQAS TTLHVNCS H CKRPMSSRGW VCDRCHRCAS MCAVCHHVVK GLFVWCQGCS HGGHLQHIMK WLEGSSHCPA GCGHLCEYS

UniProtKB: GATOR2 complex protein WDR24

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Macromolecule #3: GATOR complex protein WDR59

MacromoleculeName: GATOR complex protein WDR59 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.938391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAARWSSENV VVEFRDSQAT AMSVDCLGQH AVLSGRRFLY IVNLDAPFEG HRKISRQSKW DIGAVQWNPH DSFAHYFAAS SNQRVDLYK WKDGSGEVGT TLQGHTRVIS DLDWAVFEPD LLVTSSVDTY IYIWDIKDTR KPTVALSAVA GASQVKWNKK N ANCLATSH ...String:
MAARWSSENV VVEFRDSQAT AMSVDCLGQH AVLSGRRFLY IVNLDAPFEG HRKISRQSKW DIGAVQWNPH DSFAHYFAAS SNQRVDLYK WKDGSGEVGT TLQGHTRVIS DLDWAVFEPD LLVTSSVDTY IYIWDIKDTR KPTVALSAVA GASQVKWNKK N ANCLATSH DGDVRIWDKR KPSTAVEYLA AHLSKIHGLD WHPDSEHILA TSSQDNSVKF WDYRQPRKYL NILPCQVPVW KA RYTPFSN GLVTVMVPQL RRENSLLLWN VFDLNTPVHT FVGHDDVVLE FQWRKQKEGS KDYQLVTWSR DQTLRMWRVD SQM QRLCAN DILDGVDEFI ESISLLPEPE KTLHTEDTDH QHTASHGEEE ALKEDPPRNL LEERKSDQLG LPQTLQQEFS LINV QIRNV NVEMDAADRS CTVSVHCSNH RVKMLVKFPA QYPNNAAPSF QFINPTTITS TMKAKLLKIL KDTALQKVKR GQSCL EPCL RQLVSCLESF VNQEDSASSN PFALPNSVTP PLPTFARVTT AYGSYQDANI PFPRTSGARF CGAGYLVYFT RPMTMH RAV SPTEPTPRSL SALSAYHTGL IAPMKIRTEA PGNLRLYSGS PTRSEKEQVS ISSFYYKERK SRRWKSKREG SDSGNRQ IK AAGKVIIQDI ACLLPVHKSL GELYILNVND IQETCQKNAA SALLVGRKDL VQVWSLATVA TDLCLGPKSD PDLETPWA R HPFGRQLLES LLAHYCRLRD VQTLAMLCSV FEAQSRPQGL PNPFGPFPNR SSNLVVSHSR YPSFTSSGSC SSMSDPGLN TGGWNIAGRE AEHLSSPWGE SSPEELRFGS LTYSDPRERE RDQHDKNKRL LDPANTQQFD DFKKCYGEIL YRWGLREKRA EVLKFVSCP PDPHKGIEFG VYCSHCRSEV RGTQCAICKG FTFQCAICHV AVRGSSNFCL TCGHGGHTSH MMEWFRTQEV C PTGCGCHC LLESTF

UniProtKB: GATOR2 complex protein WDR59

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Macromolecule #4: Nucleoporin SEH1

MacromoleculeName: Nucleoporin SEH1 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.700566 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVARSIAAD HKDLIHDVSF DFHGRRMATC SSDQSVKVWD KSESGDWHCT ASWKTHSGSV WRVTWAHPEF GQVLASCSFD RTAAVWEEI VGESNDKLRG QSHWVKRTTL VDSRTSVTDV KFAPKHMGLM LATCSADGIV RIYEAPDVMN LSQWSLQHEI S CKLSCSCI ...String:
MFVARSIAAD HKDLIHDVSF DFHGRRMATC SSDQSVKVWD KSESGDWHCT ASWKTHSGSV WRVTWAHPEF GQVLASCSFD RTAAVWEEI VGESNDKLRG QSHWVKRTTL VDSRTSVTDV KFAPKHMGLM LATCSADGIV RIYEAPDVMN LSQWSLQHEI S CKLSCSCI SWNPSSSRAH SPMIAVGSDD SSPNAMAKVQ IFEYNENTRK YAKAETLMTV TDPVHDIAFA PNLGRSFHIL AI ATKDVRI FTLKPVRKEL TSSGGPTKFE IHIVAQFDNH NSQVWRVSWN ITGTVLASSG DDGCVRLWKA NYMDNWKCTG ILK GNGSPV NGSSQQGTSN PSLGSTIPSL QNSLNGSSAG RKHS

UniProtKB: Nucleoporin SEH1

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Macromolecule #5: Protein SEC13 homolog

MacromoleculeName: Protein SEC13 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.578438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSVINTVDT SHEDMIHDAQ MDYYGTRLAT CSSDRSVKIF DVRNGGQILI ADLRGHEGPV WQVAWAHPMY GNILASCSYD RKVIIWREE NGTWEKSHEH AGHDSSVNSV CWAPHDYGLI LACGSSDGAI SLLTYTGEGQ WEVKKINNAH TIGCNAVSWA P AVVPGSLI ...String:
MVSVINTVDT SHEDMIHDAQ MDYYGTRLAT CSSDRSVKIF DVRNGGQILI ADLRGHEGPV WQVAWAHPMY GNILASCSYD RKVIIWREE NGTWEKSHEH AGHDSSVNSV CWAPHDYGLI LACGSSDGAI SLLTYTGEGQ WEVKKINNAH TIGCNAVSWA P AVVPGSLI DHPSGQKPNY IKRFASGGCD NLIKLWKEEE DGQWKEEQKL EAHSDWVRDV AWAPSIGLPT STIASCSQDG RV FIWTCDD ASSNTWSPKL LHKFNDVVWH VSWSITANIL AVSGGDNKVT LWKESVDGQW VCISDVNKGQ GSVSASVTEG QQN EQ

UniProtKB: Protein SEC13 homolog

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Macromolecule #6: Cytosolic arginine sensor for mTORC1 subunit 1

MacromoleculeName: Cytosolic arginine sensor for mTORC1 subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.249238 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELHILEHRV RVLSVARPGL WLYTHPLIKL LFLPRRSRCK FFSLTETPED YTLMVDEEGF KELPPSEFLQ VAEATWLVLN VSSHSGAAV QAAGVTKIAR SVIAPLAEHH VAVLMLSTYQ TDFILVREQD LSVVIHTLAQ EFDIYREVGG EPVPVTRDDS S NGFPRTQH ...String:
MELHILEHRV RVLSVARPGL WLYTHPLIKL LFLPRRSRCK FFSLTETPED YTLMVDEEGF KELPPSEFLQ VAEATWLVLN VSSHSGAAV QAAGVTKIAR SVIAPLAEHH VAVLMLSTYQ TDFILVREQD LSVVIHTLAQ EFDIYREVGG EPVPVTRDDS S NGFPRTQH GPSPTVHPIQ SPQNRFCVLT LDPETLPAIA TTLIDVLFYS HSTPKEAASS SPEPSSITFF AFSLIEGYIS IV MDAETQK KFPSDLLLTS SSGELWRMVR IGGQPLGFDE CGIVAQIAGP LAAADISAYY ISTFNFAHAL VPEDGIGSVI EVL QRRQEG LAS

UniProtKB: Cytosolic arginine sensor for mTORC1 subunit 1

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 29 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.5
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRaw movies were imported into cryosparc2 v4.3.1 39. Patch Motion Corr. was used for motion correction and Patch CTF estimated (multi) was used for CTF determination.
Particle selectionNumber selected: 2289288
Details: Cryosparc blob picker with a diameter range of 200 A-280 A was used to generate 3,467,659 which was inspected to trim the particle set to 2,289,288 particles. Particles were extracted with a ...Details: Cryosparc blob picker with a diameter range of 200 A-280 A was used to generate 3,467,659 which was inspected to trim the particle set to 2,289,288 particles. Particles were extracted with a box size of 560x560 pixels in cryosparc2.
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3.1)
Details: Patch Motion Corr. was used for motion correction and Patch CTF estimated (multi) was used for CTF determination.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7uhy


Details: The coordinates for GATOR2 (7UHY) and arginine bound CASTOR1 (5I2C) were rigid body fitted into the composite map in UCSF ChimeraX.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1)
Details: The final particle set contained 140,606 particles and a round of homogenous refinement resulted in a 3.89 A map at 0.143 FSC.
Number images used: 140606
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. v3.3.1)
Details: A series of 2D classifications followed by an ab-initio-reconstruction was used to generate three reference maps. The resulting 3D maps were used in addition to maps generated from prior ...Details: A series of 2D classifications followed by an ab-initio-reconstruction was used to generate three reference maps. The resulting 3D maps were used in addition to maps generated from prior datasets to resort all 2289288 particles after a round of 2D classification to remove obvious junk.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.1)
Details: The final particle set contained 140,606 particles and a round of homogenous refinement resulted in a 3.89 A map at 0.143 FSC.
Final 3D classificationNumber classes: 7 / Avg.num./class: 190000 / Software - Name: cryoSPARC (ver. v3.3.1)
Details: The final particle set contained 140,606 particles and a round of homogenous refinement resulted in a 3.89 A map at 0.143 FSC.

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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

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