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- EMDB-21687: CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in th... -

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Basic information

Entry
Database: EMDB / ID: EMD-21687
TitleCryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the post-GAP state
Map dataRagulator-RagA-GDP-RagC-XDP-SLC38A9; density modified with LocScale
Sample
  • Complex: Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9
    • Complex: pentameric Ragulator
      • Protein or peptide: Ragulator complex protein LAMTOR1
      • Protein or peptide: Ragulator complex protein LAMTOR2
      • Protein or peptide: Ragulator complex protein LAMTOR3
      • Protein or peptide: Ragulator complex protein LAMTOR4
      • Protein or peptide: Ragulator complex protein LAMTOR5
    • Complex: dimeric Rag GTPases
      • Protein or peptide: Ras-related GTP-binding protein A
      • Protein or peptide: Ras-related GTP-binding protein C
    • Complex: SLC38A9
      • Protein or peptide: Sodium-coupled neutral amino acid transporter 9
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: xanthosine diphosphate
Keywordssmall GTPase / mTORC1 activation / amino acid signaling / lysosome / SIGNALING PROTEIN
Function / homology
Function and homology information


asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity / L-arginine transmembrane transporter activity / L-arginine transmembrane transport / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux ...asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity / L-arginine transmembrane transporter activity / L-arginine transmembrane transport / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / L-glutamine transmembrane transporter activity / FNIP-folliculin RagC/D GAP / Ragulator complex / glutamine transport / L-amino acid transmembrane transporter activity / L-leucine transmembrane transporter activity / protein localization to cell junction / amino acid transmembrane transport / regulation of TORC1 signaling / protein localization to lysosome / amino acid transmembrane transporter activity / regulation of TOR signaling / TORC1 signaling / endosome organization / fibroblast migration / lysosome localization / Amino acids regulate mTORC1 / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / arginine binding / enzyme-substrate adaptor activity / azurophil granule membrane / endosomal transport / cholesterol binding / small GTPase-mediated signal transduction / regulation of cell size / lysosome organization / Macroautophagy / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / tertiary granule membrane / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / RAC2 GTPase cycle / response to amino acid / RAC3 GTPase cycle / cellular response to nutrient levels / specific granule membrane / protein-membrane adaptor activity / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / positive regulation of TORC1 signaling / cellular response to starvation / cellular response to amino acid starvation / viral genome replication / RNA splicing / negative regulation of autophagy / : / cholesterol homeostasis / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / regulation of cell growth / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / MAP2K and MAPK activation / response to virus / positive regulation of protein localization to nucleus / GDP binding / late endosome / protein localization / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / late endosome membrane / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / intracellular signal transduction / protein heterodimerization activity / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / DNA-templated transcription / ubiquitin protein ligase binding
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / RagA/B / Mitogen-activated protein kinase kinase 1 interacting ...Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / RagA/B / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / Ragulator complex protein LAMTOR2-like / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR1 / Ras-related GTP-binding protein A / Neutral amino acid transporter 9 / Ras-related GTP-binding protein C / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFromm SA / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111730 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.
Authors: Simon A Fromm / Rosalie E Lawrence / James H Hurley /
Abstract: The Rag GTPases (Rags) recruit mTORC1 to the lysosomal membrane in response to nutrients, where it is then activated in response to energy and growth factor availability. The lysosomal folliculin ...The Rag GTPases (Rags) recruit mTORC1 to the lysosomal membrane in response to nutrients, where it is then activated in response to energy and growth factor availability. The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator, and the FLCN:FNIP2 (FLCN-interacting protein 2) GTPase activating protein (GAP) complex, and prevents Rag dimer activation during amino acid starvation. How the LFC is disassembled upon amino acid refeeding is an outstanding question. Here we show that the cytoplasmic tail of the human lysosomal solute carrier family 38 member 9 (SLC38A9) destabilizes the LFC and thereby triggers GAP activity of FLCN:FNIP2 toward RagC. We present the cryo-EM structures of Rags in complex with their lysosomal anchor complex Ragulator and the cytoplasmic tail of SLC38A9 in the pre- and post-GTP hydrolysis state of RagC, which explain how SLC38A9 destabilizes the LFC and so promotes Rag dimer activation.
History
DepositionApr 11, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.14
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  • Surface view with fitted model
  • Atomic models: PDB-6wj3
  • Surface level: 0.14
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21687.png

Downloads & links

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Map

FileDownload / File: emd_21687.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRagulator-RagA-GDP-RagC-XDP-SLC38A9; density modified with LocScale
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 288 pix.
= 327.456 Å		1.14 Å/pix.
x 288 pix.
= 327.456 Å		1.14 Å/pix.
x 288 pix.
= 327.456 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.137 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.2277672 - 0.56621164
Average (Standard dev.)0.0007512453 (±0.011015768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 327.456 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1371.1371.137
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z327.456327.456327.456
α/β/γ90.00090.00090.000
start NX/NY/NZ13112264
NX/NY/NZ123151209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.2280.5660.001

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Supplemental data

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Mask #1

Fileemd_21687_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_21687_msk_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_21687_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_21687_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9

EntireName: Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9
Components
  • Complex: Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9
    • Complex: pentameric Ragulator
      • Protein or peptide: Ragulator complex protein LAMTOR1
      • Protein or peptide: Ragulator complex protein LAMTOR2
      • Protein or peptide: Ragulator complex protein LAMTOR3
      • Protein or peptide: Ragulator complex protein LAMTOR4
      • Protein or peptide: Ragulator complex protein LAMTOR5
    • Complex: dimeric Rag GTPases
      • Protein or peptide: Ras-related GTP-binding protein A
      • Protein or peptide: Ras-related GTP-binding protein C
    • Complex: SLC38A9
      • Protein or peptide: Sodium-coupled neutral amino acid transporter 9
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: xanthosine diphosphate

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Supramolecule #1: Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9

SupramoleculeName: Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / Details: RagA bound to GDP, RagC bound to XDP
Molecular weightTheoretical: 170 KDa

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Supramolecule #2: pentameric Ragulator

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

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Supramolecule #3: dimeric Rag GTPases

SupramoleculeName: dimeric Rag GTPases / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: SLC38A9

SupramoleculeName: SLC38A9 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ragulator complex protein LAMTOR1

MacromoleculeName: Ragulator complex protein LAMTOR1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.32535 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
SNAEFMACCY SSENEDSDQD REERKLLLDP SSPPTKALNG AEPNYHSLPS ARTDEQALLS SILAKTASNI IDVSAADSQG MEQHEYMDR ARQYSTRLAV LSSSLTHWKK LPPLPSLTSQ PHQVLASEPI PFSDLQQVSR IAAYAYSALS QIRVDAKEEL V VQFGIP

UniProtKB: Ragulator complex protein LAMTOR1

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Macromolecule #2: Ragulator complex protein LAMTOR2

MacromoleculeName: Ragulator complex protein LAMTOR2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.645579 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GAMLRPKALT QVLSQANTGG VQSTLLLNNE GSLLAYSGYG DTDARVTAAI ASNIWAAYDR NGNQAFNEDN LKFILMDCME GRVAITRVA NLLLCMYAKE TVGFGMLKAK AQALVQYLEE PLTQVAAS

UniProtKB: Ragulator complex protein LAMTOR2

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Macromolecule #3: Ragulator complex protein LAMTOR3

MacromoleculeName: Ragulator complex protein LAMTOR3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.637678 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADDLKRFLY KKLPSVEGLH AIVVSDRDGV PVIKVANDNA PEHALRPGFL STFALATDQG SKLGLSKNKS IICYYNTYQV VQFNRLPLV VSFIASSSAN TGLIVSLEKE LAPLFEELRQ VVEVS

UniProtKB: Ragulator complex protein LAMTOR3

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Macromolecule #4: Ragulator complex protein LAMTOR4

MacromoleculeName: Ragulator complex protein LAMTOR4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.753236 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MTSALTQGLE RIPDQLGYLV LSEGAVLASS GDLENDEQAA SAISELVSTA CGFRLHRGMN VPFKRLSVVF GEHTLLVTVS GQRVFVVKR QNRGREPIDV

UniProtKB: Ragulator complex protein LAMTOR4

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Macromolecule #5: Ragulator complex protein LAMTOR5

MacromoleculeName: Ragulator complex protein LAMTOR5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.17852 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MEPGAGHLDG HRAGSPSLRQ ALCDGSAVMF SSKERGRCTV INFVPLEAPL RSTPRSRQVT EACGGEGRAV PLGSEPEWSV GGMEATLEQ HLEDTMKNPS IVGVLCTDSQ GLNLGCRGTL SDEHAGVISV LAQQAAKLTS DPTDIPVVCL ESDNGNIMIQ K HDGITVAV HKMAS

UniProtKB: Ragulator complex protein LAMTOR5

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Macromolecule #6: Ras-related GTP-binding protein A

MacromoleculeName: Ras-related GTP-binding protein A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.362078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSWSHPQFEK GGFDIDYKDD DDKMPNTAMK KKVLLMGKSG SGKTSMRSII FANYIARDTR RLGATIDVEH SHVRFLGNLV LNLWDCGGQ DTFMENYFTS QRDNIFRNVE VLIYVFDVES RELEKDMHYY QSCLEAILQN SPDAKIFCLV HKMDLVQEDQ R DLIFKERE ...String:
MSWSHPQFEK GGFDIDYKDD DDKMPNTAMK KKVLLMGKSG SGKTSMRSII FANYIARDTR RLGATIDVEH SHVRFLGNLV LNLWDCGGQ DTFMENYFTS QRDNIFRNVE VLIYVFDVES RELEKDMHYY QSCLEAILQN SPDAKIFCLV HKMDLVQEDQ R DLIFKERE EDLRRLSRPL ECACFRTSIW DETLYKAWSS IVYQLIPNVQ QLEMNLRNFA QIIEADEVLL FERATFLVIS HY QCKEQRD VHRFEKISNI IKQFKLSCSK LAASFQSMEV RNSNFAAFID IFTSNTYVMV VMSDPSIPSA ATLINIRNAR KHF EKLERV DGPKHSLLMR

UniProtKB: Ras-related GTP-binding protein A

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Macromolecule #7: Ras-related GTP-binding protein C

MacromoleculeName: Ras-related GTP-binding protein C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.758336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GADSRMSLQY GAEETPLAGS YGAADSFPKD FGYGVEEEEE EAAAAGGGVG AGAGGGCGPG GADSSKPRIL LMGLRRSGKS SIQKVVFHK MSPNETLFLE STNKIYKDDI SNSSFVNFQI WDFPGQMDFF DPTFDYEMIF RGTGALIYVI DAQDDYMEAL T RLHITVSK ...String:
GADSRMSLQY GAEETPLAGS YGAADSFPKD FGYGVEEEEE EAAAAGGGVG AGAGGGCGPG GADSSKPRIL LMGLRRSGKS SIQKVVFHK MSPNETLFLE STNKIYKDDI SNSSFVNFQI WDFPGQMDFF DPTFDYEMIF RGTGALIYVI DAQDDYMEAL T RLHITVSK AYKVNPDMNF EVFIHKVNGL SDDHKIETQR DIHQRANDDL ADAGLEKLHL SFYLTSIYDH SIFEAFSKVV QK LIPQLPT LENLLNIFIS NSGIEKAFLF DVVSKIYIAT DSSPVDMQSY ELCCDMIDVV IDVSCIYGLK EDGSGSAYDK ESM AIIKLN NTTVLYLKEV TKFLALVCIL REESFERKGL IDYNFHCFRK AIHEVFEVGV TSHRSCGHQT SASSLKALTH NGTP RNAI

UniProtKB: Ras-related GTP-binding protein C

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Macromolecule #8: Sodium-coupled neutral amino acid transporter 9

MacromoleculeName: Sodium-coupled neutral amino acid transporter 9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.610139 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GGTMANMNSD SRHLGTSEVD HERDPGPMNI QFEPSDLRSK RPFCIEPTNI VNVNHVIQRV SDHASAMNKR IHYYSRLTTP ADKALIAPD HVVPAPEECY VYSPLGSAYK LQSYTEGYGK NTS

UniProtKB: Neutral amino acid transporter 9

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Macromolecule #9: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #10: xanthosine diphosphate

MacromoleculeName: xanthosine diphosphate / type: ligand / ID: 10 / Number of copies: 1 / Formula: U3J
Molecular weightTheoretical: 444.185 Da
Chemical component information

ChemComp-U3J:
xanthosine diphosphate

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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

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 5.7 sec. / Average electron dose: 60.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2309565
Startup modelType of model: OTHER / Details: cryoSPARC v2 ab Initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 106659
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6wj3:
CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the post-GAP state

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