[English] 日本語
Yorodumi
- PDB-6swy: Structure of active GID E3 ubiquitin ligase complex minus Gid2 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6swy
TitleStructure of active GID E3 ubiquitin ligase complex minus Gid2 and delta Gid9 RING domain
Components
  • Glucose-induced degradation protein 8
  • Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10
  • Vacuolar import and degradation protein 24
  • Vacuolar import and degradation protein 28
  • Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30
KeywordsLIGASE / Suppressed / Suppreseed
Function / homology
Function and homology information


protein catabolic process in the vacuole / GID complex / ubiquitin-dependent protein catabolic process via the N-end rule pathway / ascospore formation / protein targeting to vacuole / traversing start control point of mitotic cell cycle / regulation of nitrogen utilization / vacuole / extrinsic component of membrane / negative regulation of gluconeogenesis ...protein catabolic process in the vacuole / GID complex / ubiquitin-dependent protein catabolic process via the N-end rule pathway / ascospore formation / protein targeting to vacuole / traversing start control point of mitotic cell cycle / regulation of nitrogen utilization / vacuole / extrinsic component of membrane / negative regulation of gluconeogenesis / Neutrophil degranulation / RING-type E3 ubiquitin transferase / cytoplasmic vesicle membrane / ubiquitin protein ligase activity / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / cell cycle / negative regulation of apoptotic process / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import/degradation protein Vid24 ...Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / LIS1 homology (LisH) motif profile. / LIS1 homology motif / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Armadillo-like helical / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar import and degradation protein 24 / Glucose-induced degradation protein 8 / Protein FYV10 / Vacuolar import and degradation protein 28 / Vacuolar import and degradation protein 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsQiao, S. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2020
Title: Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly.
Authors: Shuai Qiao / Christine R Langlois / Jakub Chrustowicz / Dawafuti Sherpa / Ozge Karayel / Fynn M Hansen / Viola Beier / Susanne von Gronau / Daniel Bollschweiler / Tillman Schäfer / Arno F ...Authors: Shuai Qiao / Christine R Langlois / Jakub Chrustowicz / Dawafuti Sherpa / Ozge Karayel / Fynn M Hansen / Viola Beier / Susanne von Gronau / Daniel Bollschweiler / Tillman Schäfer / Arno F Alpi / Matthias Mann / J Rajan Prabu / Brenda A Schulman /
Abstract: Cells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, in Saccharomyces cerevisiae, carbon stress-induced ...Cells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, in Saccharomyces cerevisiae, carbon stress-induced gluconeogenesis is terminated upon glucose availability, a process that involves the multiprotein E3 ligase GID recruiting N termini and catalyzing ubiquitylation of gluconeogenic enzymes. Here, genetics, biochemistry, and cryoelectron microscopy define molecular underpinnings of glucose-induced degradation. Unexpectedly, carbon stress induces an inactive anticipatory complex (GID), which awaits a glucose-induced substrate receptor to form the active GID. Meanwhile, other environmental perturbations elicit production of an alternative substrate receptor assembling into a related E3 ligase complex. The intricate structure of GID enables anticipating and ultimately binding various N-degron-targeting (i.e., "N-end rule") substrate receptors, while the GID E3 forms a clamp-like structure juxtaposing substrate lysines with the ubiquitylation active site. The data reveal evolutionarily conserved GID complexes as a family of multisubunit E3 ubiquitin ligases responsive to extracellular stimuli.
History
DepositionSep 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / em_software / entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_torsion / software / struct_conf / struct_ref / struct_ref_seq / struct_sheet_range
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_software.category / _em_software.fitting_id / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_polymer_linkage.dist / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model orientation/position / Details: Re-build coordinates from A336-S347 in Chain 4. / Provider: author / Type: Coordinate replacement

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10333
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
5: Vacuolar import and degradation protein 28
8: Glucose-induced degradation protein 8
1: Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30
4: Vacuolar import and degradation protein 24
9: Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10


Theoretical massNumber of molelcules
Total (without water)370,4815
Polymers370,4815
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Vacuolar import and degradation protein 28 / Glucose-induced degradation protein 5


Mass: 105658.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VID28, GID5, YIL017C
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P40547
#2: Protein Glucose-induced degradation protein 8 / Dosage-dependent cell cycle regulator 1


Mass: 51789.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: GID8, DCR1, YMR135C, YM9375.04C
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P40208
#3: Protein Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30 / Glucose-induced degradation protein 1


Mass: 117308.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast), (gene. exp.) Saccharomyces cerevisiae S288C (yeast)
Gene: VID30, GID1, YGL227W
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P53076
#4: Protein Vacuolar import and degradation protein 24 / Glucose-induced degradation protein 4


Mass: 41291.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: VID24, GID4, YBR105C, YBR0834
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P38263
#5: Protein Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10 / Function required for yeast viability protein 10 / Glucose-induced degradation protein 9 / Probable ...Function required for yeast viability protein 10 / Glucose-induced degradation protein 9 / Probable E3 ubiquitin-protein ligase GID9


Mass: 54432.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast), (gene. exp.) Saccharomyces cerevisiae S288C (yeast)
Gene: FYV10, GID9, YIL097W
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P40492, RING-type E3 ubiquitin transferase
Compound detailsFor residue numbers above 3000 could potentially correspond to the indicated chain, although their ...For residue numbers above 3000 could potentially correspond to the indicated chain, although their precise positions and identities are ambiguous.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: GIDSR4 minus Gid2/delta Gid9RING / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288C and YJM1133
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 6.5
SpecimenConc.: 0.25 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 54.48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122248 / Symmetry type: POINT

+
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