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- EMDB-62292: cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb -

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Basic information

Entry
Database: EMDB / ID: EMD-62292
Titlecryo-EM structure of TRIP12 in complex with K29/48 branched-triUb
Map data
Sample
  • Complex: TRIP12 in complex with K29/48 triUb probe
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin K29C
    • Protein or peptide: E3 ubiquitin-protein ligase TRIP12
KeywordsHECT E3 ligase / Branching / K29/48 / LIGASE
Function / homology
Function and homology information


heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / nuclear thyroid hormone receptor binding / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / DNA repair-dependent chromatin remodeling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis ...heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / nuclear thyroid hormone receptor binding / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / DNA repair-dependent chromatin remodeling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / regulation of embryonic development / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / 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 / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / 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 / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling
Similarity search - Function
E3 ubiquitin-protein ligase HECTD1/TRIP12-like / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / S27a-like superfamily ...E3 ubiquitin-protein ligase HECTD1/TRIP12-like / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / E3 ubiquitin-protein ligase TRIP12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsAi HS / Wu XW / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, 22407121, T2488301, 22277073 and 92253302 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination.
Authors: Xiangwei Wu / Huasong Ai / Junxiong Mao / Hongyi Cai / Lu-Jun Liang / Zebin Tong / Zhiheng Deng / Qingyun Zheng / Lei Liu / Man Pan /
Abstract: The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ...The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ubiquitination to K48-linked ubiquitin chains to augment polyubiquitination. How HECT-E3 ligase Ufd4 mediates the ubiquitination event remains unclear. Here, we biochemically determine that Ufd4 preferentially catalyses K29-linked ubiquitination on K48-linked ubiquitin chains to generate K29/K48-branched ubiquitin chains and capture structural snapshots of Ub transfer cascades for Ufd4-mediated ubiquitination. The N-terminal ARM region and HECT domain C-lobe of Ufd4 are identified and characterized as key structural elements that together recruit K48-linked diUb and orient Lys29 of its proximal Ub to the active cysteine of Ufd4 for K29-linked branched ubiquitination. These structures not only provide mechanistic insights into the architecture of the Ufd4 complex but also provide structural visualization of branched ubiquitin chain formation by a HECT-type E3 ligase.
History
DepositionNov 5, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62292.png

Downloads & links

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Map

FileDownload / File: emd_62292.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.032703333 - 0.0514193
Average (Standard dev.)0.00012721613 (±0.0014625589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 206.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_62292_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_62292_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62292_half_map_2.map
Projections & Slices
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Sample components

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Entire : TRIP12 in complex with K29/48 triUb probe

EntireName: TRIP12 in complex with K29/48 triUb probe
Components
  • Complex: TRIP12 in complex with K29/48 triUb probe
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin K29C
    • Protein or peptide: E3 ubiquitin-protein ligase TRIP12

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Supramolecule #1: TRIP12 in complex with K29/48 triUb probe

SupramoleculeName: TRIP12 in complex with K29/48 triUb probe / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 1 / 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: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #2: Ubiquitin K29C

MacromoleculeName: Ubiquitin K29C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.550794 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKACI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #3: E3 ubiquitin-protein ligase TRIP12

MacromoleculeName: E3 ubiquitin-protein ligase TRIP12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180.781953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGT SDDSEMGRLQ ALLEARGLPP HLFGPLGPRM SQLFHRTIGS GASSKAQQLL QGLQASDESQ QLQAVIEMCQ LLVMGNEET LGGFPVKSVV PALITLLQME HNFDIMNHAC RALTYMMEAL PRSSAVVVDA IPVFLEKLQV IQCIDVAEQA L TALEMLSR ...String:
DYKDDDDKGT SDDSEMGRLQ ALLEARGLPP HLFGPLGPRM SQLFHRTIGS GASSKAQQLL QGLQASDESQ QLQAVIEMCQ LLVMGNEET LGGFPVKSVV PALITLLQME HNFDIMNHAC RALTYMMEAL PRSSAVVVDA IPVFLEKLQV IQCIDVAEQA L TALEMLSR RHSKAILQAG GLADCLLYLE FFSINAQRNA LAIAANCCQS ITPDEFHFVA DSLPLLTQRL THQDKKSVES TC LCFARLV DNFQHEENLL QQVASKDLLT NVQQLLVVTP PILSSGMFIM VVRMFSLMCS NCPTLAVQLM KQNIAETLHF LLC GASNGS CQEQIDLVPR SPQELYELTS LICELMPCLP KEGIFAVDTM LKKGNAQNTD GAIWQWRDDR GLWHPYNRID SRII EQINE DTGTARAIQR KPNPLANSNT SGYSESKKDD ARAQLMKEDP ELAKSFIKTL FGVLYEVYSS SAGPAVRHKC LRAIL RIIY FADAELLKDV LKNHAVSSHI ASMLSSQDLK IVVGALQMAE ILMQKLPDIF SVYFRREGVM HQVKHLAESE SLLTSP PKA CTNGSGSMGS TTSVSSGTAT AATHAAADLG SPSLQHSRDD SLDLSPQGRL SDVLKRKRLP KRGPRRPKYS PPRDDDK VD NQAKSPTTTQ SPKSSFLASL NPKTWGRLST QSNSNNIEPA RTAGGSGLAR AASKDTISNN REKIKGWIKE QAHKFVER Y FSSENMDGSN PALNVLQRLC AATEQLNLQV DGGAECLVEI RSIVSESDVS SFEIQHSGFV KQLLLYLTSK SEKDAVSRE IRLKRFLHVF FSSPLPGEEP IGRVEPVGNA PLLALVHKMN NCLSQMEQFP VKVHDFPSGN GTGGSFSLNR GSQALKFFNT HQLKCQLQR HPDCANVKQW KGGPVKIDPL ALVQAIERYL VVRGYGRVRE DDEDSDDDGS DEEIDESLAA QFLNSGNVRH R LQFYIGEH LLPYNMTVYQ AVRQFSIQAE DERESTDDES NPLGRAGIWT KTHTIWYKPV REDEESNKDC VGGKRGRAQT AP TKTSPRN AKKHDELWHD GVCPSVSNPL EVYLIPTPPE NITFEDPSLD VILLLRVLHA ISRYWYYLYD NAMCKEIIPT SEF INSKLT AKANRQLQDP LVIMTGNIPT WLTELGKTCP FFFPFDTRQM LFYVTAFDRD RAMQRLLDTN PEINQSDSQD SRVA PRLDR KKRTVNREEL LKQAESVMQD LGSSRAMLEI QYENEVGTGL GPTLEFYALV SQELQRADLG LWRGEEVTLS NPKGS QEGT KYIQNLQGLF ALPFGRTAKP AHIAKVKMKF RFLGKLMAKA IMDFRLVDLP LGLPFYKWML RQETSLTSHD LFDIDP VVA RSVYHLEDIV RQKKRLEQDK SQTKESLQYA LETLTMNGCS VEDLGLDFTL PGFPNIELKK GGKDIPVTIH NLEEYLR LV IFWALNEGVS RQFDSFRDGF ESVFPLSHLQ YFYPEELDQL LCGSKADTWD AKTLMECCRP DHGYTHDSRA VKFLFEIL S SFDNEQQRLF LQFVTGSPRL PVGGFRSLNP PLTIVRKTFE STENPDDFLP SVMTCVNYLK LPDYSSIEIM REKLLIAAR EGQQSFHLS

UniProtKB: E3 ubiquitin-protein ligase TRIP12

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 259711
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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