[English] 日本語
Yorodumi
- PDB-9lvj: Cryo-EM structure of Sestrin2 bound human GATOR2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lvj
TitleCryo-EM structure of Sestrin2 bound human GATOR2 complex
Components
  • (GATOR2 complex protein ...) x 3
  • Isoform B of Nucleoporin SEH1
  • Protein SEC13 homolog
  • Sestrin-2
KeywordsSIGNALING PROTEIN / Amino acid sensor
Function / homology
Function and homology information


oligodendrocyte progenitor proliferation / regulation of response to reactive oxygen species / sulfiredoxin activity / negative regulation of translation in response to endoplasmic reticulum stress / GATOR2 complex / L-leucine binding / Atg1/ULK1 kinase complex / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding ...oligodendrocyte progenitor proliferation / regulation of response to reactive oxygen species / sulfiredoxin activity / negative regulation of translation in response to endoplasmic reticulum stress / GATOR2 complex / L-leucine binding / Atg1/ULK1 kinase complex / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / central nervous system myelin formation / TORC2 complex / COPII-coated vesicle cargo loading / PH domain binding / cellular response to leucine starvation / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / mitochondrial DNA metabolic process / nucleotide-activated protein kinase complex / 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 / cellular response to L-leucine / Amino acids regulate mTORC1 / protein K6-linked ubiquitination / attachment of mitotic spindle microtubules to kinetochore / 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 / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / vacuolar membrane / GDP-dissociation inhibitor activity / positive regulation of lipophagy / nucleocytoplasmic transport / triglyceride homeostasis / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / cellular oxidant detoxification / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / fatty acid beta-oxidation / regulation of cAMP/PKA signal transduction / Vpr-mediated nuclear import of PICs / D-glucose import / regulation of protein phosphorylation / oligodendrocyte differentiation / positive regulation of macroautophagy / SUMOylation of DNA replication proteins / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / mRNA transport / response to glucose / nuclear pore / SUMOylation of DNA damage response and repair proteins / cellular response to nutrient levels / cellular response to glucose starvation / negative regulation of TORC1 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / signaling adaptor activity / Mitotic Prometaphase / positive regulation of TORC1 signaling / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / cellular response to amino acid starvation / reactive oxygen species metabolic process / protein sequestering activity / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / TP53 Regulates Metabolic Genes / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DNA damage response, signal transduction by p53 class mediator / cellular response to amino acid stimulus / intracellular protein transport / peroxidase activity / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / ER to Golgi transport vesicle membrane / negative regulation of cell growth / response to insulin / RING-type E3 ubiquitin transferase / kinetochore / autophagy / ISG15 antiviral mechanism / positive regulation of protein localization to nucleus
Similarity search - Function
Sestrin / PA26 p53-induced protein (sestrin) / WDR59, modified RING finger, H2 subclass (C3H3C2-type) / MIOS, WD40 repeat / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid ...Sestrin / PA26 p53-induced protein (sestrin) / WDR59, modified RING finger, H2 subclass (C3H3C2-type) / MIOS, WD40 repeat / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid / : / : / RING/Ubox like zinc-binding domain / AhpD-like / RWD domain profile. / RWD / RWD domain / Sec13/Seh1 family / 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 / Sestrin-2 / GATOR2 complex protein WDR59 / Nucleoporin SEH1 / GATOR2 complex protein WDR24 / GATOR2 complex protein MIOS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsSu, M.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government20231120103446003 China
CitationJournal: Cell Rep / Year: 2025
Title: Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex.
Authors: Ming-Yuan Su / Fei Teng / Shan Wang / Xinyi Mai / Huan Zeng / Juan Li / Xiaoxiao Song / Xi Wang / Goran Stjepanovic /
Abstract: Mammalian cells regulate growth by integrating environmental cues through the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The human GATOR2 complex, comprising WDR59, WDR24, ...Mammalian cells regulate growth by integrating environmental cues through the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The human GATOR2 complex, comprising WDR59, WDR24, Mios, Sec13, and Seh1l, is key to mTORC1 regulation. Under amino acid deprivation, GATOR2 is inhibited through interactions with cytosolic leucine sensor Sestrin2 and arginine sensor cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1). Amino acid abundance relieves this inhibition, allowing GATOR2 to antagonize the repressor GATOR1. Despite its importance, GATOR2's inhibition mechanisms were unclear. Here, we present cryo-electron microscopy (cryo-EM) structures of GATOR2 in three inhibitory states: CASTOR1 bound, Sestrin2 bound, and dual bound. CASTOR1 engages the Mios WD40 β-propellers, while Sestrin2 interacts with the WDR24-Seh1l subcomplex, inducing conformational movements. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) reveals dynamic motions in apo-GATOR2 and its complexes with amino acid sensors, as well as the effects of amino acid supplementation. These findings unravel the interactions between GATOR2 and amino acid sensors, providing a perspective on the regulation of the mTORC1 pathway by nutrient-sensing machinery.
History
DepositionFeb 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GATOR2 complex protein MIOS
B: GATOR2 complex protein MIOS
C: GATOR2 complex protein WDR24
D: GATOR2 complex protein WDR59
E: Isoform B of Nucleoporin SEH1
F: Isoform B of Nucleoporin SEH1
G: Isoform B of Nucleoporin SEH1
H: Protein SEC13 homolog
K: GATOR2 complex protein MIOS
L: GATOR2 complex protein MIOS
M: GATOR2 complex protein WDR24
N: GATOR2 complex protein WDR59
O: Isoform B of Nucleoporin SEH1
P: Isoform B of Nucleoporin SEH1
Q: Isoform B of Nucleoporin SEH1
R: Protein SEC13 homolog
U: Sestrin-2
V: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,94850
Polymers1,261,85418
Non-polymers2,09332
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
GATOR2 complex protein ... , 3 types, 8 molecules ABKLCMDN

#1: Protein
GATOR2 complex protein MIOS


Mass: 98700.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIOS / Production host: Homo sapiens (human) / References: UniProt: Q9NXC5
#2: Protein GATOR2 complex protein WDR24


Mass: 88326.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR24 / Production host: Homo sapiens (human) / References: UniProt: Q96S15
#3: Protein GATOR2 complex protein WDR59 / WD repeat-containing protein 59


Mass: 109938.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR59, KIAA1923, FP977 / Production host: Homo sapiens (human) / References: UniProt: Q6PJI9

-
Protein , 3 types, 10 molecules EFGOPQHRUV

#4: Protein
Isoform B of Nucleoporin SEH1 / GATOR2 complex protein SEH1 / Nup107-160 subcomplex subunit SEH1 / SEC13-like protein


Mass: 46636.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEH1L, SEC13L, SEH1 / Production host: Homo sapiens (human) / References: UniProt: Q96EE3
#5: Protein Protein SEC13 homolog


Mass: 40791.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC13 / Production host: Homo sapiens (human) / References: UniProt: P55735
#6: Protein Sestrin-2


Mass: 54560.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SESN2 / Production host: Homo sapiens (human) / References: UniProt: P58004

-
Non-polymers , 1 types, 32 molecules

#7: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Sestrin2 bound human GATOR2 complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.73 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 48.41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Details: The movies consist of 50 frames, with a total dose of 48.41 e-/A2, 48.41 e-/A2, or 52.41 e-/A2

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190375 / Symmetry type: POINT
RefinementHighest resolution: 3.82 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00648685
ELECTRON MICROSCOPYf_angle_d0.73166974
ELECTRON MICROSCOPYf_dihedral_angle_d4.4667839
ELECTRON MICROSCOPYf_chiral_restr0.0468120
ELECTRON MICROSCOPYf_plane_restr0.0068903

+
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://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