[English] 日本語
Yorodumi
- EMDB-12560: Catalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12560
TitleCatalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase
Map data
Sample
  • Complex: Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9
    • Protein or peptide: E3 ubiquitin-protein ligase RMD5
    • Protein or peptide: Protein FYV10
  • Ligand: ZINC ION
KeywordsGID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM / LIGASE
Function / homology
Function and homology information


GID complex / Regulation of pyruvate metabolism / negative regulation of gluconeogenesis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / peroxisome / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of apoptotic process ...GID complex / Regulation of pyruvate metabolism / negative regulation of gluconeogenesis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / peroxisome / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of apoptotic process / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Rmd5, degenerated RING (dRING) finger / Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
GID complex subunit 9 / E3 ubiquitin-protein ligase RMD5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSherpa D / Chrustowicz J / Prabu JR / Schulman BA
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Citation
Journal: Mol Cell / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme.
Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / ...Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / Matthias Mann / Arno F Alpi / Brenda A Schulman /
Abstract: How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of ...How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GID, which resembles an organometallic supramolecular chelate. The Chelator-GID assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.
#1: Journal: Biorxiv / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme
Authors: Sherpa D / Chrustowicz J / Qiao S / Langlois CR / Hehl LA / Gottemukkala KV / Hansen FM / Karayel O / Prabu JR / Mann M / Alpi AF / Schulman BA
History
DepositionMar 5, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ns4
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12560.png

Downloads & links

-
Map

FileDownload / File: emd_12560.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 288 pix.
= 455.04 Å		1.58 Å/pix.
x 288 pix.
= 455.04 Å		1.58 Å/pix.
x 288 pix.
= 455.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.18229897 - 0.2407837
Average (Standard dev.)0.000024366449 (±0.0023474123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 455.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z455.040455.040455.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1820.2410.000

-
Supplemental data

-
Mask #1

Fileemd_12560_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12560_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12560_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9

EntireName: Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9
Components
  • Complex: Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9
    • Protein or peptide: E3 ubiquitin-protein ligase RMD5
    • Protein or peptide: Protein FYV10
  • Ligand: ZINC ION

-
Supramolecule #1: Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9

SupramoleculeName: Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Generated by focused refinement of Chelator-GID SR4 + Fbp1 map
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 110 KDa

-
Macromolecule #1: E3 ubiquitin-protein ligase RMD5

MacromoleculeName: E3 ubiquitin-protein ligase RMD5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 49.244594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSELLDSFET EFAKFYTDSN LEETNLQKCL DHTHEFKSQL KKLKAHLNKH IQESKPEVYN KLSDKEKQKF KRKRELIIEK LSKSQRQWD HSVKKQIKYV SQQSNRFNKS TLNKLKEFDI DSVYVNKLPK ETMENVNEAI GYHILRYSID NMPLGNKNEA F QYLKDVYG ...String:
MSELLDSFET EFAKFYTDSN LEETNLQKCL DHTHEFKSQL KKLKAHLNKH IQESKPEVYN KLSDKEKQKF KRKRELIIEK LSKSQRQWD HSVKKQIKYV SQQSNRFNKS TLNKLKEFDI DSVYVNKLPK ETMENVNEAI GYHILRYSID NMPLGNKNEA F QYLKDVYG ITNKESTEFI EMGQIVHDLK KGDTESCLKW CSNEMESLSS NHTALSSLKF DLYTLSAMQI VKHGNPVELY YQ ITQNAPL DCFRHREKEL MQNVVPLLTK SLIGQPIEDI DSKVNKELKE CTSLFIKEYC AAKHIFFDSP LFLIVLSGLI SFQ FFIKYK TIRELAHVDW TTKDELPFDV KLPDFLTHFH PIFICPVLKE ETTTENPPYS LACHHIISKK ALDRLSKNGT ITFK CPYCP VNTSMSSTKK VRFVML

UniProtKB: E3 ubiquitin-protein ligase RMD5

-
Macromolecule #2: Protein FYV10

MacromoleculeName: Protein FYV10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 59.975102 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAEKSIFNEP DVDFHLKLNQ QLFHIPYELL SKRIKHTQAV INKETKSLHE HTAALNQIFE HNDVEHDELA LAKITEMIRK VDHIERFLN TQIKSYCQIL NRIKKRLEFF HELKDIKSQN SGTSHNGNNE GTRTKLIQWY QSYTNILIGD YLTRNNPIKY N SETKDHWN ...String:
MAEKSIFNEP DVDFHLKLNQ QLFHIPYELL SKRIKHTQAV INKETKSLHE HTAALNQIFE HNDVEHDELA LAKITEMIRK VDHIERFLN TQIKSYCQIL NRIKKRLEFF HELKDIKSQN SGTSHNGNNE GTRTKLIQWY QSYTNILIGD YLTRNNPIKY N SETKDHWN SGVVFLKQSQ LDDLIDYDVL LEANRISTSL LHERNLLPLI SWINENKKTL TKKSSILEFQ ARLQEYIELL KV DNYTDAI VCFQRFLLPF VKSNFTDLKL ASGLLIFIKY CNDQKPTSST SSGFDTEEIK SQSLPMKKDR IFQHFFHKSL PRI TSKPAV NTTDYDKSSL INLQSGDFER YLNLLDDQRW SVLNDLFLSD FYSMYGISQN DPLLIYLSLG ISSLKTRDCL HPSD DENGN QETETATTAE KEVEDLQLFT LHSLKRKNCP VCSETFKPIT QALPFAHHIQ SQLFENPILL PNGNVYDSKK LKKLA KTLK KQNLISLNPG QIMDPVDMKI FCESDSIKMY PT

UniProtKB: GID complex subunit 9

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 79.2 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

12557

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74254
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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