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- EMDB-20814: Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20814
TitleCryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex
Map data
Sample
  • Complex: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases and the scaffolding protein complex Ragulator
    • Protein or peptide: x 9 types
  • Ligand: x 3 types
Function / homology
Function and homology information


negative regulation of cell proliferation involved in kidney development / cell proliferation involved in kidney development / negative regulation of post-translational protein modification / 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 / FNIP-folliculin RagC/D GAP ...negative regulation of cell proliferation involved in kidney development / cell proliferation involved in kidney development / negative regulation of post-translational protein modification / 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 / FNIP-folliculin RagC/D GAP / Ragulator complex / negative regulation of brown fat cell differentiation / regulation of Ras protein signal transduction / protein localization to cell junction / regulation of TORC1 signaling / regulation of pro-B cell differentiation / negative regulation of lysosome organization / protein localization to lysosome / regulation of TOR signaling / TORC1 signaling / endosome organization / fibroblast migration / lysosome localization / Amino acids regulate mTORC1 / ATPase inhibitor activity / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / negative regulation of TOR signaling / cell-cell junction assembly / negative regulation of glycolytic process / enzyme-substrate adaptor activity / enzyme inhibitor activity / negative regulation of cold-induced thermogenesis / negative regulation of Rho protein signal transduction / azurophil granule membrane / endosomal transport / small GTPase-mediated signal transduction / regulation of cell size / lysosome organization / Macroautophagy / positive regulation of transforming growth factor beta receptor signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / tertiary granule membrane / hemopoiesis / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / centriolar satellite / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / RAC2 GTPase cycle / response to amino acid / TOR signaling / RAC3 GTPase cycle / cellular response to nutrient levels / positive regulation of intrinsic apoptotic signaling pathway / specific granule membrane / positive regulation of autophagy / protein-membrane adaptor activity / energy homeostasis / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / cellular response to starvation / cellular response to amino acid starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / RNA splicing / viral genome replication / transforming growth factor beta receptor signaling pathway / negative regulation of autophagy / : / cholesterol homeostasis / epithelial cell proliferation / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / phosphoprotein binding / positive regulation of protein-containing complex assembly / regulation of protein phosphorylation / MAP2K and MAPK activation / response to virus / cilium / mitotic spindle / negative regulation of ERK1 and ERK2 cascade / positive regulation of protein localization to nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of epithelial cell proliferation / GDP binding
Similarity search - Function
Folliculin / Folliculin, DENN domain / Folliculin, DENN domain, C-terminal superfamily / Folliculin C-terminal domain / Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminus / Folliculin-interacting protein middle domain ...Folliculin / Folliculin, DENN domain / Folliculin, DENN domain, C-terminal superfamily / Folliculin C-terminal domain / Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminus / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile. / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / 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 / Folliculin / Ras-related GTP-binding protein C / Folliculin-interacting protein 2 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsShen K / Rogala KB / Yu ZH / Sabatini DM
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA103866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R37 AI47389 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA129105 United States
Lustgarten Foundation United States
Department of Defense (DOD, United States)W81XWH-15-1-0230 United States
Tuberous Sclerosis Association United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.
Authors: Kuang Shen / Kacper B Rogala / Hui-Ting Chou / Rick K Huang / Zhiheng Yu / David M Sabatini /
Abstract: mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN- ...mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway.
History
DepositionOct 8, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-6ulg
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20814.png

Downloads & links

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Map

FileDownload / File: emd_20814.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002 / Movie #1: 0.02
Minimum - Maximum-0.058811273 - 0.10569042
Average (Standard dev.)0.000012088260 (±0.0023958504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0590.1060.000

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Supplemental data

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Sample components

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Entire : Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases an...

EntireName: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases and the scaffolding protein complex Ragulator
Components
  • Complex: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases and the scaffolding protein complex Ragulator
    • Protein or peptide: Folliculin
    • Protein or peptide: Ragulator complex protein LAMTOR3
    • Protein or peptide: Ragulator complex protein LAMTOR2
    • Protein or peptide: Ragulator complex protein LAMTOR5
    • Protein or peptide: Ragulator complex protein LAMTOR4
    • Protein or peptide: Ragulator complex protein LAMTOR1
    • Protein or peptide: Ras-related GTP-binding protein A
    • Protein or peptide: Ras-related GTP-binding protein C
    • Protein or peptide: Folliculin-interacting protein 2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases an...

SupramoleculeName: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases and the scaffolding protein complex Ragulator
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Folliculin

MacromoleculeName: Folliculin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.551191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNAIVALCHF CELHGPRTLF CTEVLHAPLP QGDGNEDSPG QGEQAEEEEG GIQMNSRMRA HSPAEGASVE SSSPGPKKSD MCEGCRSLA AGHPGYISHD KETSIKYVSH QHPSHPQLFS IVRQACVRSL SCEVCPGREG PIFFGDEQHG FVFSHTFFIK D SLARGFQR ...String:
MNAIVALCHF CELHGPRTLF CTEVLHAPLP QGDGNEDSPG QGEQAEEEEG GIQMNSRMRA HSPAEGASVE SSSPGPKKSD MCEGCRSLA AGHPGYISHD KETSIKYVSH QHPSHPQLFS IVRQACVRSL SCEVCPGREG PIFFGDEQHG FVFSHTFFIK D SLARGFQR WYSIITIMMD RIYLINSWPF LLGKVRGIID ELQGKALKVF EAEQFGCPQR AQRMNTAFTP FLHQRNGNAA RS LTSLTSD DNLWACLHTS FAWLLKACGS RLTEKLLEGA PTEDTLVQME KLADLEEESE SWDNSEAEEE EKAPVLPEST EGR ELTQGP AESSSLSGCG SWQPRKLPVF KSLRHMRQVL GAPSFRMLAW HVLMGNQVIW KSRDVDLVQS AFEVLRTMLP VGCV RIIPY SSQYEEAYRC NFLGLSPHVQ IPPHVLSSEF AVIVEVHAAA RSTLHPVGCE DDQSLSKYEF VVTSGSPVAA DRVGP TILN KIEAALTNQN LSVDVVDQCL VCLKEEWMNK VKVLFKFTKV DSRPKEDTQK LLSILGASEE DNVKLLKFWM TGLSKT YKS HLMSTVRSPT ASESRN

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Macromolecule #2: Ragulator complex protein LAMTOR3

MacromoleculeName: Ragulator complex protein LAMTOR3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.637678 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADDLKRFLY KKLPSVEGLH AIVVSDRDGV PVIKVANDNA PEHALRPGFL STFALATDQG SKLGLSKNKS IICYYNTYQV VQFNRLPLV VSFIASSSAN TGLIVSLEKE LAPLFEELRQ VVEVS

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Macromolecule #3: Ragulator complex protein LAMTOR2

MacromoleculeName: Ragulator complex protein LAMTOR2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.51745 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLRPKALTQV LSQANTGGVQ STLLLNNEGS LLAYSGYGDT DARVTAAIAS NIWAAYDRNG NQAFNEDNLK FILMDCMEGR VAITRVANL LLCMYAKETV GFGMLKAKAQ ALVQYLEEPL TQVAAS

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Macromolecule #4: Ragulator complex protein LAMTOR5

MacromoleculeName: Ragulator complex protein LAMTOR5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.6229 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEATLEQHLE DTMKNPSIVG VLCTDSQGLN LGCRGTLSDE HAGVISVLAQ QAAKLTSDPT DIPVVCLESD NGNIMIQKHD GITVAVHKM AS

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Macromolecule #5: Ragulator complex protein LAMTOR4

MacromoleculeName: Ragulator complex protein LAMTOR4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.753236 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTSALTQGLE RIPDQLGYLV LSEGAVLASS GDLENDEQAA SAISELVSTA CGFRLHRGMN VPFKRLSVVF GEHTLLVTVS GQRVFVVKR QNRGREPIDV

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Macromolecule #6: Ragulator complex protein LAMTOR1

MacromoleculeName: Ragulator complex protein LAMTOR1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.762775 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGCCYSSENE DSDQDREERK LLLDPSSPPT KALNGAEPNY HSLPSARTDE QALLSSILAK TASNIIDVSA ADSQGMEQHE YMDRARQYS TRLAVLSSSL THWKKLPPLP SLTSQPHQVL ASEPIPFSDL QQVSRIAAYA YSALSQIRVD AKEELVVQFG I P

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

MacromoleculeName: Ras-related GTP-binding protein A / type: protein_or_peptide / ID: 7 / Details: RagA containing a T21N mutation / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.628168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPNTAMKKKV LLMGKSGSGK NSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGQDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET ...String:
MPNTAMKKKV LLMGKSGSGK NSMRSIIFAN 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

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Macromolecule #8: Ras-related GTP-binding protein C

MacromoleculeName: Ras-related GTP-binding protein C / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.271832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKSSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN ...String:
MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKSSIQKV 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

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Macromolecule #9: Folliculin-interacting protein 2

MacromoleculeName: Folliculin-interacting protein 2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.260195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPTLLQKLF NKRGSSGSSA AASAQGRAPK EGPAFSWSCS EFDLNEIRLI VYQDCDRRGR QVLFDSKAVQ KIEEVTAQKT EDVPIKISA KCCQGSSSVS SSSSSSISSH SSSGGSSHHA KEQLPKYQYT RPASDVNMLG EMMFGSVAMS YKGSTLKIHY I RSPPQLMI ...String:
MAPTLLQKLF NKRGSSGSSA AASAQGRAPK EGPAFSWSCS EFDLNEIRLI VYQDCDRRGR QVLFDSKAVQ KIEEVTAQKT EDVPIKISA KCCQGSSSVS SSSSSSISSH SSSGGSSHHA KEQLPKYQYT RPASDVNMLG EMMFGSVAMS YKGSTLKIHY I RSPPQLMI SKVFSARMGS FCGSTNNLQD SFEYINQDPN LGKLNTNQNS LGPCRTGSNL AHSTPVDMPS RGQNEDRDSG IA RSASLSS LLITPFPSPS SSTSSSSSYQ RRWLRSQTTS LENGIIPRRS TDETFSLAEE TCSSNPAMVR RKKIAISIIF SLC EKEEAQ RNFQDFFFSH FPLFESHMNR LKSAIEKAMI SCRKIAESSL RVQFYVSRLM EALGEFRGTI WNLYSVPRIA EPVW LTMMS GTLEKNQLCQ RFLKEFTLLI EQINKNQFFA ALLTAVLTYH LAWVPTVMPV DHPPIKAFSE KRTSQSVNML AKTHP YNPL WAQLGDLYGA IGSPVRLTRT VVVGKQKDLV QRILYVLTYF LRCSELQENQ LTWSGNHGEG DQVLNGSKII TALEKG EVE ESEYVVITVR NEPALVPPIL PPTAAERHNP WPTGFPECPE GTDSRDLGLK PDKEANRRPE QGSEACSAGC LGPASDA SW KPQNAFCGDE KNKEAPQDGS SRLPSCEVLG AGMKMDQQAV CELLKVEMPT RLPDRSVAWP CPDRHLREKP SLEKVTFQ I GSFASPESDF ESRMKKMEER VKACGPSLEA SEAADVAQDP QVSRSPFKPG FQENVCCPQN RLSEGDEGES DKGFAEDRG SRNDMAADIA GQLSHAADLG TASHGAGGTG GRRLEATRGL YVKAAEGPVL EPVAPRCVQR GPGLVAGANI PCGDDNKKAN FRTEGDIPR NESSDSALGD SDDEACASAM LDLGHGGDRT GGSLEVELPL PRSQSISTQN VRNFGRSLLA GYCPTYMPDL V LHGTGSDE KLKQCLVADL VHTVHHPVLD EPIAEAVCII ADTDKWSVQV ATSQRKVTDN MKLGQDVLVS SQVSSLLQSI LQ LYKLHLP ADFCIMHLED RLQEMYLKSK MLSEYLRGHT RVHVKELGVV LGIESNDLPL LTAIASTHSP YVAQILL

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Macromolecule #10: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / 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 #11: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 11 / Number of copies: 1 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration8 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 59.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126984
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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