[English] 日本語
Yorodumi
- EMDB-0554: Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0554
TitleCryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator)
Map datagenerated by non-uniform refinement from cryoSPARC v2 followed by LocScale amplitude scaling
Sample
  • Complex: FLCN-FNIP2-RagA-RagC-Ragulator Complex
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
Function / homology
Function and homology information


negative regulation of cell proliferation involved in kidney development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / 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 / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / 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 / negative regulation of lysosome organization / regulation of pro-B cell differentiation / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / ATPase inhibitor activity / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / enzyme-substrate adaptor activity / negative regulation of glycolytic process / enzyme inhibitor activity / negative regulation of TOR signaling / cell-cell junction assembly / negative regulation of cold-induced thermogenesis / negative regulation of Rho protein signal transduction / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / small GTPase-mediated signal transduction / lysosome organization / positive regulation of transforming growth factor beta receptor signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / hemopoiesis / ficolin-1-rich granule membrane / centriolar satellite / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to amino acid / positive regulation of autophagy / specific granule membrane / energy homeostasis / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / ERK1 and ERK2 cascade / cellular response to amino acid starvation / cellular response to starvation / negative regulation of autophagy / viral genome replication / intrinsic apoptotic signaling pathway / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / transforming growth factor beta receptor signaling pathway / guanyl-nucleotide exchange factor activity / epithelial cell proliferation / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / regulation of protein phosphorylation / positive regulation of protein-containing complex assembly / response to virus / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / negative regulation of ERK1 and ERK2 cascade / mitotic spindle / cilium / positive regulation of protein localization to nucleus / 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 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: 3.6 Å
AuthorsFromm SA / Young LN / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM111730-05 United States
CitationJournal: Science / Year: 2019
Title: Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex.
Authors: Rosalie E Lawrence / Simon A Fromm / Yangxue Fu / Adam L Yokom / Do Jin Kim / Ashley M Thelen / Lindsey N Young / Chun-Yan Lim / Avi J Samelson / James H Hurley / Roberto Zoncu /
Abstract: The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) ...The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) activating protein (GAP) activity toward the GTPase RagC. Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. To determine the lysosomal function of FLCN, we reconstituted the human lysosomal FLCN complex (LFC) containing FLCN, its partner FLCN-interacting protein 2 (FNIP2), and the RagA:RagC GTPases as they exist in the starved state with their lysosomal anchor Ragulator complex and determined its cryo-electron microscopy structure to 3.6 angstroms. The RagC-GAP activity of FLCN was inhibited within the LFC, owing to displacement of a catalytically required arginine in FLCN from the RagC nucleotide. Disassembly of the LFC and release of the RagC-GAP activity of FLCN enabled mTORC1-dependent regulation of the master regulator of lysosomal biogenesis, transcription factor E3, implicating the LFC as a checkpoint in mTORC1 signaling.
History
DepositionFeb 13, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseNov 6, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nzd
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0554.png

Downloads & links

-
Map

FileDownload / File: emd_0554.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgenerated by non-uniform refinement from cryoSPARC v2 followed by LocScale amplitude scaling
Voxel sizeX=Y=Z: 1.149 Å
Density
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.36063316 - 0.79141235
Average (Standard dev.)0.00061260565 (±0.0105887605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 413.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1491.1491.149
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z413.640413.640413.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.3610.7910.001

-
Supplemental data

-
Additional map: generated by non-uniform refinement from cryoSPARC v2 followed...

Fileemd_0554_additional_1.map
Annotationgenerated by non-uniform refinement from cryoSPARC v2 followed by the cryoSPARC v2 local filtering/sharpening routine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: generated by non-uniform refinement from cryoSPARC v2 followed...

Fileemd_0554_additional_2.map
Annotationgenerated by non-uniform refinement from cryoSPARC v2 followed by the Relion3-beta PostProcess routine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : FLCN-FNIP2-RagA-RagC-Ragulator Complex

EntireName: FLCN-FNIP2-RagA-RagC-Ragulator Complex
Components
  • Complex: FLCN-FNIP2-RagA-RagC-Ragulator Complex
    • 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: Hepatitis B virus x interacting protein
    • Protein or peptide: Ras-related GTP-binding protein A
    • Protein or peptide: Ras-related GTP-binding protein C
    • Protein or peptide: Folliculin
    • Protein or peptide: Folliculin-interacting protein 2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione

+
Supramolecule #1: FLCN-FNIP2-RagA-RagC-Ragulator Complex

SupramoleculeName: FLCN-FNIP2-RagA-RagC-Ragulator Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 / Details: RagA bound to GDP; RagC bound to XTPgammaS
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

+
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

+
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

+
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

+
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

+
Macromolecule #5: Hepatitis B virus x interacting protein

MacromoleculeName: Hepatitis B virus x interacting protein / 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

+
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: 36.615168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

+
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

+
Macromolecule #8: Folliculin

MacromoleculeName: Folliculin / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.14307 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMNAIVAL CHFCELHGPR TLFCTEVLHA PLPQGDGNED SPGQGEQAE EEEGGIQMNS RMRAHSPAEG ASVESSSPGP KKSDMCEGCR SLAAGHPGYI SHDKETSIKY VSHQHPSHPQ L FSIVRQAC ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMNAIVAL CHFCELHGPR TLFCTEVLHA PLPQGDGNED SPGQGEQAE EEEGGIQMNS RMRAHSPAEG ASVESSSPGP KKSDMCEGCR SLAAGHPGYI SHDKETSIKY VSHQHPSHPQ L FSIVRQAC VRSLSCEVCP GREGPIFFGD EQHGFVFSHT FFIKDSLARG FQRWYSIITI MMDRIYLINS WPFLLGKVRG II DELQGKA LKVFEAEQFG CPQRAQRMNT AFTPFLHQRN GNAARSLTSL TSDDNLWACL HTSFAWLLKA CGSRLTEKLL EGA PTEDTL VQMEKLADLE EESESWDNSE AEEEEKAPVL PESTEGRELT QGPAESSSLS GCGSWQPRKL PVFKSLRHMR QVLG APSFR MLAWHVLMGN QVIWKSRDVD LVQSAFEVLR TMLPVGCVRI IPYSSQYEEA YRCNFLGLSP HVQIPPHVLS SEFAV IVEV HAAARSTLHP VGCEDDQSLS KYEFVVTSGS PVAADRVGPT ILNKIEAALT NQNLSVDVVD QCLVCLKEEW MNKVKV LFK FTKVDSRPKE DTQKLLSILG ASEEDNVKLL KFWMTGLSKT YKSHLMSTVR SPTASESRN

+
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: 122.475414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGTMAPTLLQ KLFNKRGSSG SSAAASAQGR APKEGPAFSW SCSEFDLNEI RLIVYQDCDR RGRQVLFDSK AVQKIEEVTA QKTEDVPIK ISAKCCQGSS SVSSSSSSSI SSHSSSGGSS HHAKEQLPKY QYTRPASDVN MLGEMMFGSV AMSYKGSTLK I HYIRSPPQ ...String:
GGTMAPTLLQ KLFNKRGSSG SSAAASAQGR APKEGPAFSW SCSEFDLNEI RLIVYQDCDR RGRQVLFDSK AVQKIEEVTA QKTEDVPIK ISAKCCQGSS SVSSSSSSSI SSHSSSGGSS HHAKEQLPKY QYTRPASDVN MLGEMMFGSV AMSYKGSTLK I HYIRSPPQ LMISKVFSAR MGSFCGSTNN LQDSFEYINQ DPNLGKLNTN QNSLGPCRTG SNLAHSTPVD MPSRGQNEDR DS GIARSAS LSSLLITPFP SPSSSTSSSS SYQRRWLRSQ TTSLENGIIP RRSTDETFSL AEETCSSNPA MVRRKKIAIS IIF SLCEKE EAQRNFQDFF FSHFPLFESH MNRLKSAIEK AMISCRKIAE SSLRVQFYVS RLMEALGEFR GTIWNLYSVP RIAE PVWLT MMSGTLEKNQ LCQRFLKEFT LLIEQINKNQ FFAALLTAVL TYHLAWVPTV MPVDHPPIKA FSEKRTSQSV NMLAK THPY NPLWAQLGDL YGAIGSPVRL TRTVVVGKQK DLVQRILYVL TYFLRCSELQ ENQLTWSGNH GEGDQVLNGS KIITAL EKG EVEESEYVVI TVRNEPALVP PILPPTAAER HNPWPTGFPE CPEGTDSRDL GLKPDKEANR RPEQGSEACS AGCLGPA SD ASWKPQNAFC GDEKNKEAPQ DGSSRLPSCE VLGAGMKMDQ QAVCELLKVE MPTRLPDRSV AWPCPDRHLR EKPSLEKV T FQIGSFASPE SDFESRMKKM EERVKACGPS LEASEAADVA QDPQVSRSPF KPGFQENVCC PQNRLSEGDE GESDKGFAE DRGSRNDMAA DIAGQLSHAA DLGTASHGAG GTGGRRLEAT RGLYVKAAEG PVLEPVAPRC VQRGPGLVAG ANIPCGDDNK KANFRTEGD IPRNESSDSA LGDSDDEACA SAMLDLGHGG DRTGGSLEVE LPLPRSQSIS TQNVRNFGRS LLAGYCPTYM P DLVLHGTG SDEKLKQCLV ADLVHTVHHP VLDEPIAEAV CIIADTDKWS VQVATSQRKV TDNMKLGQDV LVSSQVSSLL QS ILQLYKL HLPADFCIMH LEDRLQEMYL KSKMLSEYLR GHTRVHVKEL GVVLGIESND LPLLTAIAST HSPYVAQILL

+
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

+
Macromolecule #11: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}...

MacromoleculeName: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione
type: ligand / ID: 11 / Number of copies: 1 / Formula: L8S
Molecular weightTheoretical: 540.231 Da
Chemical component information

ChemComp-L8S:
9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
25.0 mMHEPES
130.0 mMsodium chlorideNaCl
2.5 mMmagnesium chlorideMgCl2
2.0 mMEGTA
0.5 mMTCEP
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Details: 15 W
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Whatman 597.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2703 / Average exposure time: 11.0 sec. / Average electron dose: 65.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 982343
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: NONE / Details: cryoSPARC v2 ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 163376
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6b9x

chain_id: A

6b9x

chain_id: B

6b9x

chain_id: C

6b9x

chain_id: D

6b9x

chain_id: E

6ehr

chain_id: E, residue_range: 48-68

6ces

chain_id: A

6ces

chain_id: C

3v42

chain_id: B

3llu

chain_id: A, residue_range: 119-139
RefinementSpace: REAL
Output model

PDB-6nzd:
Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more