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- EMDB-17764: Catalytic module of yeast GID E3 ligase bound to multiphosphoryla... -

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Entry
Database: EMDB / ID: EMD-17764
TitleCatalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin
Map data
Sample
  • Complex: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
    • Protein or peptide: E3 ubiquitin-protein ligase RMD5
    • Protein or peptide: Protein FYV10
    • Protein or peptide: Ubiquitin-conjugating enzyme E2-24 kDa
    • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
KeywordsE3 ubiquitin ligase / E2 ubiquitin-conjugating enzyme / phosphorylation / GID / LIGASE
Function / homology
Function and homology information


GID complex / mitochondrial outer membrane translocase complex assembly / Regulation of pyruvate metabolism / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of gluconeogenesis / Maturation of protein E / Maturation of protein E ...GID complex / mitochondrial outer membrane translocase complex assembly / Regulation of pyruvate metabolism / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of gluconeogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling / Activation of NF-kappaB in B cells / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / EGFR downregulation
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. / Ubiquitin-conjugating enzyme, active site ...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. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2-24 kDa / GID complex subunit 9 / E3 ubiquitin-protein ligase RMD5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsChrustowicz J / Sherpa D / Prabu RJ / Schulman BA
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)H2020 789016-NEDD8ActivateEuropean Union
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: Mol Cell / Year: 2024
Title: Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies.
Authors: Jakub Chrustowicz / Dawafuti Sherpa / Jerry Li / Christine R Langlois / Eleftheria C Papadopoulou / D Tung Vu / Laura A Hehl / Özge Karayel / Viola Beier / Susanne von Gronau / Judith ...Authors: Jakub Chrustowicz / Dawafuti Sherpa / Jerry Li / Christine R Langlois / Eleftheria C Papadopoulou / D Tung Vu / Laura A Hehl / Özge Karayel / Viola Beier / Susanne von Gronau / Judith Müller / J Rajan Prabu / Matthias Mann / Gary Kleiger / Arno F Alpi / Brenda A Schulman /
Abstract: Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ...Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ubiquitin ligases and their dedicated E2, Ubc8/UBE2H (yeast/human nomenclature). GID/CTLH-Ubc8/UBE2H-mediated ubiquitylation regulates biological processes ranging from yeast metabolic signaling to human development. Here, cryoelectron microscopy (cryo-EM), biochemistry, and cell biology reveal this exquisitely specific E3-E2 pairing through an unconventional catalytic assembly and auxiliary interactions 70-100 Å away, mediated by E2 multisite phosphorylation. Rather than dynamic polyelectrostatic interactions reported for other ubiquitylation complexes, multiple Ubc8/UBE2H phosphorylation sites within acidic CK2-targeted sequences specifically anchor the E2 C termini to E3 basic patches. Positions of phospho-dependent interactions relative to the catalytic domains correlate across evolution. Overall, our data show that phosphorylation-dependent multivalency establishes a specific E3-E2 partnership, is antagonistic with dephosphorylation, rigidifies the catalytic centers within a flexing GID E3-substrate assembly, and facilitates substrate collision with ubiquitylation active sites.
History
DepositionJun 29, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17764.png

Downloads & links

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Map

FileDownload / File: emd_17764.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 272 pix.
= 388.144 Å		1.43 Å/pix.
x 272 pix.
= 388.144 Å		1.43 Å/pix.
x 272 pix.
= 388.144 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.427 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0348
Minimum - Maximum-0.123829156 - 0.23513684
Average (Standard dev.)0.00003761115 (±0.0028035343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 388.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17764_msk_1.map
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Additional map: Map post-processed with DeepEMhancer

Fileemd_17764_additional_1.map
AnnotationMap post-processed with DeepEMhancer
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Half map: #2

Fileemd_17764_half_map_1.map
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Half map: #1

Fileemd_17764_half_map_2.map
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Sample components

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Entire : Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 subst...

EntireName: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
Components
  • Complex: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
    • Protein or peptide: E3 ubiquitin-protein ligase RMD5
    • Protein or peptide: Protein FYV10
    • Protein or peptide: Ubiquitin-conjugating enzyme E2-24 kDa
    • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION

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Supramolecule #1: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 subst...

SupramoleculeName: Complex of yeast Chelator-GIDSR4 E3 ligase, tetrameric Fbp1 substrate and multiphosphorylated Ubc8~ubiquitin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Map obtained by focus refinement over the catalytic module (Gid2, Gid9) and Ubc8~ubiquitin
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.7 MDa

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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 (brewer's yeast)
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

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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 (brewer's yeast)
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

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Macromolecule #3: Ubiquitin-conjugating enzyme E2-24 kDa

MacromoleculeName: Ubiquitin-conjugating enzyme E2-24 kDa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.920771 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSSKRRIET DVMKLLMSDH QVDLINDSMQ EFHVKFLGPK DTPYENGVWR LHVELPDNYP YKSPSIGFVN KIFHPNIDIA SGSIKLDVI NSTWSPLYDL INIVEWMIPG LLKEPNGSDP LNNEAATLQL RDKKLYEEKI KEYIDKYATK EKYQQMFGGD N DSDDSDSG ...String:
MSSSKRRIET DVMKLLMSDH QVDLINDSMQ EFHVKFLGPK DTPYENGVWR LHVELPDNYP YKSPSIGFVN KIFHPNIDIA SGSIKLDVI NSTWSPLYDL INIVEWMIPG LLKEPNGSDP LNNEAATLQL RDKKLYEEKI KEYIDKYATK EKYQQMFGGD N DSDDSDSG GDLQEEDSDS DEDMDGTGVS SGDDSVDEL(SEP) EDL(SEP)DIDV(SEP)D DDDYDEVANQ

UniProtKB: Ubiquitin-conjugating enzyme E2-24 kDa

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Macromolecule #4: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

12557

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80606
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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