[English] 日本語
Yorodumi
- EMDB-50182: cryo-EM structure of human LST2 bound to human mTOR complex 1, fo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50182
Titlecryo-EM structure of human LST2 bound to human mTOR complex 1, focused on RAPTOR
Map data
Sample
  • Complex: mTORC1 in complex with LST2
    • Protein or peptide: Regulatory-associated protein of mTOR
    • Protein or peptide: Lateral signaling target protein 2 homolog
KeywordsMTOR / MTORC1 / LST2 / ZFYVE28 / EGFR / TOS / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of epidermal growth factor-activated receptor activity / positive regulation of pentose-phosphate shunt / TORC1 complex / TORC1 signaling / positive regulation of odontoblast differentiation / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / phosphatidylinositol-3-phosphate binding ...negative regulation of epidermal growth factor-activated receptor activity / positive regulation of pentose-phosphate shunt / TORC1 complex / TORC1 signaling / positive regulation of odontoblast differentiation / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / phosphatidylinositol-3-phosphate binding / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / enzyme-substrate adaptor activity / positive regulation of transcription by RNA polymerase III / regulation of cell size / Macroautophagy / negative regulation of epidermal growth factor receptor signaling pathway / protein kinase activator activity / mTORC1-mediated signalling / social behavior / HSF1-dependent transactivation / positive regulation of TOR signaling / TOR signaling / cellular response to nutrient levels / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of lipid biosynthetic process / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / cellular response to starvation / positive regulation of glycolytic process / negative regulation of autophagy / positive regulation of peptidyl-threonine phosphorylation / regulation of autophagy / Regulation of PTEN gene transcription / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / cellular response to amino acid stimulus / small GTPase binding / cytoplasmic stress granule / positive regulation of peptidyl-serine phosphorylation / protein-macromolecule adaptor activity / early endosome membrane / cellular response to hypoxia / positive regulation of cell growth / lysosome / response to xenobiotic stimulus / lysosomal membrane / neuronal cell body / dendrite / DNA damage response / protein-containing complex binding / protein kinase binding / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Lateral signaling target protein 2, FYVE domain / : / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related ...Lateral signaling target protein 2, FYVE domain / : / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / HEAT repeat / HEAT repeat / Zinc finger, FYVE/PHD-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Regulatory-associated protein of mTOR / Lateral signaling target protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsCraigie LM / Maier T
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation179323 Switzerland
H2020 Marie Curie Actions of the European Commission812830European Union
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: mTORC1 phosphorylates and stabilizes LST2 to negatively regulate EGFR
Authors: Battaglioni S / Craigie LM / Filippini S / Maier T / Hall MN
History
DepositionApr 26, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_50182.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.5929286 - 3.2557654
Average (Standard dev.)0.00013283736 (±0.02694005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 670.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : mTORC1 in complex with LST2

EntireName: mTORC1 in complex with LST2
Components
  • Complex: mTORC1 in complex with LST2
    • Protein or peptide: Regulatory-associated protein of mTOR
    • Protein or peptide: Lateral signaling target protein 2 homolog

-
Supramolecule #1: mTORC1 in complex with LST2

SupramoleculeName: mTORC1 in complex with LST2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Regulatory-associated protein of mTOR

MacromoleculeName: Regulatory-associated protein of mTOR / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 152.764656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHHHHH EQKLISEEDL DYKDDDDKME SEMLQSPLLG LGEEDEADLT DWNLPLAFMK KRHCEKIEGS KSLAQSWRMK DRMKTVSVA LVLCLNVGVD PPDVVKTTPC ARLECWIDPL SMGPQKALET IGANLQKQYE NWQPRARYKQ SLDPTVDEVK K LCTSLRRN ...String:
HHHHHHHHHH EQKLISEEDL DYKDDDDKME SEMLQSPLLG LGEEDEADLT DWNLPLAFMK KRHCEKIEGS KSLAQSWRMK DRMKTVSVA LVLCLNVGVD PPDVVKTTPC ARLECWIDPL SMGPQKALET IGANLQKQYE NWQPRARYKQ SLDPTVDEVK K LCTSLRRN AKEERVLFHY NGHGVPRPTV NGEVWVFNKN YTQYIPLSIY DLQTWMGSPS IFVYDCSNAG LIVKSFKQFA LQ REQELEV AAINPNHPLA QMPLPPSMKN CIQLAACEAT ELLPMIPDLP ADLFTSCLTT PIKIALRWFC MQKCVSLVPG VTL DLIEKI PGRLNDRRTP LGELNWIFTA ITDTIAWNVL PRDLFQKLFR QDLLVASLFR NFLLAERIMR SYNCTPVSSP RLPP TYMHA MWQAWDLAVD ICLSQLPTII EEGTAFRHSP FFAEQLTAFQ VWLTMGVENR NPPEQLPIVL QVLLSQVHRL RALDL LGRF LDLGPWAVSL ALSVGIFPYV LKLLQSSARE LRPLLVFIWA KILAVDSSCQ ADLVKDNGHK YFLSVLADPY MPAEHR TMT AFILAVIVNS YHTGQEACLQ GNLIAICLEQ LNDPHPLLRQ WVAICLGRIW QNFDSARWCG VRDSAHEKLY SLLSDPI PE VRCAAVFALG TFVGNSAERT DHSTTIDHNV AMMLAQLVSD GSPMVRKELV VALSHLVVQY ESNFCTVALQ FIEEEKNY A LPSPATTEGG SLTPVRDSPC TPRLRSVSSY GNIRAVATAR SLNKSLQNLS LTEESGGAVA FSPGNLSTSS SASSTLGSP ENEEHILSFE TIDKMRRASS YSSLNSLIGV SFNSVYTQIW RVLLHLAADP YPEVSDVAMK VLNSIAYKAT VNARPQRVLD TSSLTQSAP ASPTNKGVHI HQAGGSPPAS STSSSSLTND VAKQPVSRDL PSGRPGTTGP AGAQYTPHSH QFPRTRKMFD K GPEQTADD ADDAAGHKSF ISATVQTGFC DWSARYFAQP VMKIPEEHDL ESQIRKEREW RFLRNSRVRR QAQQVIQKGI TR LDDQIFL NRNPGVPSVV KFHPFTPCIA VADKDSICFW DWEKGEKLDY FHNGNPRYTR VTAMEYLNGQ DCSLLLTATD DGA IRVWKN FADLEKNPEM VTAWQGLSDM LPTTRGAGMV VDWEQETGLL MSSGDVRIVR IWDTDREMKV QDIPTGADSC VTSL SCDSH RSLIVAGLGD GSIRVYDRRM ALSECRVMTY REHTAWVVKA SLQKRPDGHI VSVSVNGDVR IFDPRMPESV NVLQI VKGL TALDIHPQAD LIACGSVNQF TAIYNSSGEL INNIKYYDGF MGQRVGAISC LAFHPHWPHL AVGSNDYYIS VYSVEK RVR

UniProtKB: Regulatory-associated protein of mTOR

-
Macromolecule #2: Lateral signaling target protein 2 homolog

MacromoleculeName: Lateral signaling target protein 2 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.604477 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMNRFRKWLY KPKRSDPQLL ARFYYADEEL NQVAAELDSL DGRKDPQRCT LLVSQFRSCQ DNVLNIINQI MDECIPQDRA PRDFCVKFP EEIRHDNLAG QLWFGAECLA AGSIIMNREL ESMAMRPLAK ELTRSLEDVR GALRDQALRD LNTYTEKMRE A LRHFDVLF ...String:
MMNRFRKWLY KPKRSDPQLL ARFYYADEEL NQVAAELDSL DGRKDPQRCT LLVSQFRSCQ DNVLNIINQI MDECIPQDRA PRDFCVKFP EEIRHDNLAG QLWFGAECLA AGSIIMNREL ESMAMRPLAK ELTRSLEDVR GALRDQALRD LNTYTEKMRE A LRHFDVLF AEFELSYVSA MVPVKSPREY YVQQEVIVLF CETVERALDF GYLTQDMIDD YEPALMFSIP RLAIVCGLVV YA DGPLNLD RKVEDMSELF RPFHTLLRKI RDLLQTLTEE ELHTLERNLC ISQDVEFPIR ADVQGPAALA PALSAPLPPE GPL SAKAKD PDAELACSMQ YDDQELEQLS RMVHRAGDEM SSLLSPPIAC QSPAHRPGAE GSPGGEASPG RPRLRSGSDE EERV FFMDD VEGTAEALAR PESPAGPFGW AGSTWADPQE KGQGGPGGAA GISLPASEKE EDLSNNNLEA EGTDGASLAG TSSCS CLDS RLHLDGWEVG ADDAETAEMI AHRTGGMKLS ATVIFNPKSP TSLDSAVATQ EAASEPVAEG MDGGPHKLST GATNCL LHS CVCCGSCGDS REDVVERLRE KCSPGGVIGA SYAAGLAKAS DRAPERQEEA PPPSEDASNG REPKAPTSDK CLPHTSG SQ VDTASGLQGE AGVAGQQEPE ARELHAGSPS AHEAPQALSG SSSSTAGSCS SDKMGPEAAP AATHAAPQAT REKIRSRF H GSHDLIHRLF VCISGVADQL QTNYASDLRS ILKTLFEVMA TKPETDDKEK LRKVTQTLRS AALEDCALCQ ETLSSSELA AKTRDGDFED PPEWVPDEAC GFCTACKAPF TVIRRKHHCR SCGKIFCSRC SSHSAPLPRY GQVKPVRVCT HCYMFHVTPF YSDKAGL

UniProtKB: Lateral signaling target protein 2 homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4719 / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1057805
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 545524
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

Initial modelPDB ID:

7peb


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9f43:
cryo-EM structure of human LST2 bound to human mTOR complex 1, focused on RAPTOR

+
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://pdbjlc1.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