[English] 日本語
Yorodumi
- EMDB-12564: Substrate receptor scaffolding module of human CTLH E3 ubiquitin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12564
TitleSubstrate receptor scaffolding module of human CTLH E3 ubiquitin ligase
Map data
Sample
  • Complex: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
    • Protein or peptide: Ran-binding protein 9
    • Protein or peptide: Isoform 2 of Armadillo repeat-containing protein 8
    • Protein or peptide: Glucose-induced degradation protein 8 homolog
    • Protein or peptide: Glucose-induced degradation protein 4 homolog
KeywordsGID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM / LIGASE
Function / homology
Function and homology information


GID complex / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / Regulation of pyruvate metabolism / negative regulation of ERK1 and ERK2 cascade ...GID complex / L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / Regulation of pyruvate metabolism / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / small GTPase binding / specific granule lumen / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / cell junction / tertiary granule lumen / RAF/MAP kinase cascade / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / Neutrophil degranulation / enzyme binding / protein homodimerization activity / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / 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 / LisH ...Ran binding protein 9/10, SPRY domain / Armadillo-type fold containing protein ARMC8/Vid28 / 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 / LisH / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Armadillo-like helical / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Armadillo repeat-containing protein 8 / Glucose-induced degradation protein 4 homolog / Ran-binding protein 9 / Glucose-induced degradation protein 8 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChrustowicz J / Sherpa D / 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 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nsc
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12564.png

Downloads & links

-
Map

FileDownload / File: emd_12564.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 352 pix.
= 299.2 Å		0.85 Å/pix.
x 352 pix.
= 299.2 Å		0.85 Å/pix.
x 352 pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0245 / Movie #1: 0.0245
Minimum - Maximum-0.07453973 - 0.12510686
Average (Standard dev.)0.00008618144 (±0.0022115025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z299.200299.200299.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0750.1250.000

-
Supplemental data

-
Mask #1

Fileemd_12564_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_12564_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12564_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12564_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 a...

EntireName: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
Components
  • Complex: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
    • Protein or peptide: Ran-binding protein 9
    • Protein or peptide: Isoform 2 of Armadillo repeat-containing protein 8
    • Protein or peptide: Glucose-induced degradation protein 8 homolog
    • Protein or peptide: Glucose-induced degradation protein 4 homolog

-
Supramolecule #1: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 a...

SupramoleculeName: SRS module of human CTLH complex comprising RANBP9, TWA1, ARMC8 and hGid4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Generated by focused refinement of CTLH SR4 map
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

-
Macromolecule #1: Ran-binding protein 9

MacromoleculeName: Ran-binding protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.927062 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSGQPPPPPP QQQQQQQQLS PPPPAALAPV SGVVLPAPPA VSAGSSPAGS PGGGAGGEGL GAAAAALLLH PPPPPPPATA APPPPPPPP PPPASAAAPA SGPPAPPGLA AGPGPAGGAP TPALVAGSSA AAPFPHGDSA LNEQEKELQR RLKRLYPAVD E QETPLPRS ...String:
MSGQPPPPPP QQQQQQQQLS PPPPAALAPV SGVVLPAPPA VSAGSSPAGS PGGGAGGEGL GAAAAALLLH PPPPPPPATA APPPPPPPP PPPASAAAPA SGPPAPPGLA AGPGPAGGAP TPALVAGSSA AAPFPHGDSA LNEQEKELQR RLKRLYPAVD E QETPLPRS WSPKDKFSYI GLSQNNLRVH YKGHGKTPKD AASVRATHPI PAACGIYYFE VKIVSKGRDG YMGIGLSAQG VN MNRLPGW DKHSYGYHGD DGHSFCSSGT GQPYGPTFTT GDVIGCCVNL INNTCFYTKN GHSLGIAFTD LPPNLYPTVG LQT PGEVVD ANFGQHPFVF DIEDYMREWR TKIQAQIDRF PIGDREGEWQ TMIQKMVSSY LVHHGYCATA EAFARSTDQT VLEE LASIK NRQRIQKLVL AGRMGEAIET TQQLYPSLLE RNPNLLFTLK VRQFIEMVNG TDSEVRCLGG RSPKSQDSYP VSPRP FSSP SMSPSHGMNI HNLASGKGST AHFSGFESCS NGVISNKAHQ SYCHSNKHQS SNLNVPELNS INMSRSQQVN NFTSND VDM ETDHYSNGVG ETSSNGFLNG SSKHDHEMED CDTEMEVDSS QLRRQLCGGS QAAIERMIHF GRELQAMSEQ LRRDCGK NT ANKKMLKDAF SLLAYSDPWN SPVGNQLDPI QREPVCSALN SAILETHNLP KQPPLALAMG QATQCLGLMA RSGIGSCA F ATVEDYLH

UniProtKB: Ran-binding protein 9

-
Macromolecule #2: Isoform 2 of Armadillo repeat-containing protein 8

MacromoleculeName: Isoform 2 of Armadillo repeat-containing protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.082297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEVTASSRHY VDRLFDPDPQ KVLQGVIDMK NAVIGNNKQK ANLIVLGAVP RLLYLLQQET SSTELKTECA VVLGSLAMGT ENNVKSLLD CHIIPALLQG LLSPDLKFIE ACLRCLRTIF TSPVTPEELL YTDATVIPHL MALLSRSRYT QEYICQIFSH C CKGPDHQT ...String:
MEVTASSRHY VDRLFDPDPQ KVLQGVIDMK NAVIGNNKQK ANLIVLGAVP RLLYLLQQET SSTELKTECA VVLGSLAMGT ENNVKSLLD CHIIPALLQG LLSPDLKFIE ACLRCLRTIF TSPVTPEELL YTDATVIPHL MALLSRSRYT QEYICQIFSH C CKGPDHQT ILFNHGAVQN IAHLLTSLSY KVRMQALKCF SVLAFENPQV SMTLVNVLVD GELLPQIFVK MLQRDKPIEM QL TSAKCLT YMCRAGAIRT DDNCIVLKTL PCLVRMCSKE RLLEERVEGA ETLAYLIEPD VELQRIASIT DHLIAMLADY FKY PSSVSA ITDIKRLDHD LKHAHELRQA AFKLYASLGA NDEDIRKKII ETENMMDRIV TGLSESSVKV RLAAVRCLHS LSRS VQQLR TSFQDHAVWK PLMKVLQNAP DEILVVASSM LCNLLLEFSP SKEPILESGA VELLCGLTQS ENPALRVNGI WALMN MAFQ AEQKIKADIL RSLSTEQLFR LLSDSDLNVL MKTLGLLRNL LSTRPHIDKI MSTHGKQIMQ AVTLILEGEH NIEVKE QTL CILANIADGT TAKDLIMTND DILQKIKYYM GHSHVKLQLA AMFCISNLIW NEEEGSQERQ DKLRDMGIVD ILHKLSQ SP DSNLCDKAKM ALQQYLA

UniProtKB: Armadillo repeat-containing protein 8

-
Macromolecule #3: Glucose-induced degradation protein 8 homolog

MacromoleculeName: Glucose-induced degradation protein 8 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.796715 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYAEKPDEI TKDEWMEKLN NLHVQRADMN RLIMNYLVTE GFKEAAEKFR MESGIEPSVD LETLDERIKI REMILKGQIQ EAIALINSL HPELLDTNRY LYFHLQQQHL IELIRQRETE AALEFAQTQL AEQGEESREC LTEMERTLAL LAFDSPEESP F GDLLHTMQ ...String:
MSYAEKPDEI TKDEWMEKLN NLHVQRADMN RLIMNYLVTE GFKEAAEKFR MESGIEPSVD LETLDERIKI REMILKGQIQ EAIALINSL HPELLDTNRY LYFHLQQQHL IELIRQRETE AALEFAQTQL AEQGEESREC LTEMERTLAL LAFDSPEESP F GDLLHTMQ RQKVWSEVNQ AVLDYENRES TPKLAKLLKL LLWAQNELDQ KKVKYPKMTD LSKGVIEEPK SDENLYFQSG WS HPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: Glucose-induced degradation protein 8 homolog

-
Macromolecule #4: Glucose-induced degradation protein 4 homolog

MacromoleculeName: Glucose-induced degradation protein 4 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.559906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MCARGQVGRG TQLRTGRPCS QVPGSRWRPE RLLRRQRAGG RPSRPHPARA RPGLSLPATL LGSRAAAAVP LPLPPALAPG DPAMPVRTE CPPPAGASAA SAASLIPPPP INTQQPGVAT SLLYSGSKFR GHQKSKGNSY DVEVVLQHVD TGNSYLCGYL K IKGLTEEY ...String:
MCARGQVGRG TQLRTGRPCS QVPGSRWRPE RLLRRQRAGG RPSRPHPARA RPGLSLPATL LGSRAAAAVP LPLPPALAPG DPAMPVRTE CPPPAGASAA SAASLIPPPP INTQQPGVAT SLLYSGSKFR GHQKSKGNSY DVEVVLQHVD TGNSYLCGYL K IKGLTEEY PTLTTFFEGE IISKKHPFLT RKWDADEDVD RKHWGKFLAF YQYAKSFNSD DFDYEELKNG DYVFMRWKEQ FL VPDHTIK DISGASFAGF YYICFQKSAA SIEGYYYHRS SEWYQSLNLT HVPEHSAPIY EFR

UniProtKB: Glucose-induced degradation protein 4 homolog

-
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: 60.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78264
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