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- EMDB-16356: Structure of HECT E3 UBR5 forming K48 linked Ubiquitin chains -

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Basic information

Entry
Database: EMDB / ID: EMD-16356
TitleStructure of HECT E3 UBR5 forming K48 linked Ubiquitin chains
Map dataDeepEMhancer sharpened Focussed refinement map
Sample
  • Complex: HECT E3 UBR5 forming K48 linked Ubiquitin chains
    • Protein or peptide: E3 ubiquitin-protein ligase UBR5
    • Protein or peptide: Polyubiquitin-B
    • Protein or peptide: Polyubiquitin-B
  • Ligand: 5-azanylpentan-2-one
KeywordsE3 ligase / UBR5 / Ubiquitination / UBQ / Ubiquitin / HECT / K48 / UBQ-chain / polyubiquitylation / LIGASE
Function / homology
Function and homology information


heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / hypothalamus gonadotrophin-releasing hormone neuron development / DNA repair-dependent chromatin remodeling / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / ubiquitin-ubiquitin ligase activity / fat pad development / female gonad development ...heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / hypothalamus gonadotrophin-releasing hormone neuron development / DNA repair-dependent chromatin remodeling / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / ubiquitin-ubiquitin ligase activity / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / progesterone receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K48-linked ubiquitination / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NF-kB is activated and signals survival / Regulation of PTEN localization / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / neuron projection morphogenesis / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Recognition of DNA damage by PCNA-containing replication complex
Similarity search - Function
: / E3 ubiquitin ligase EDD, ubiquitin-associated domain / E3 ubiquitin ligase EDD / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Zinc finger, UBR-type / Zinc finger UBR-type profile. ...: / E3 ubiquitin ligase EDD, ubiquitin-associated domain / E3 ubiquitin ligase EDD / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5 / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHehl LA / Prabu JR / Schulman BA
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Chem Biol / Year: 2024
Title: Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5.
Authors: Laura A Hehl / Daniel Horn-Ghetko / J Rajan Prabu / Ronnald Vollrath / D Tung Vu / David A Pérez Berrocal / Monique P C Mulder / Gerbrand J van der Heden van Noort / Brenda A Schulman /
Abstract: Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron ...Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
History
DepositionDec 16, 2022-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16356.png

Downloads & links

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Map

FileDownload / File: emd_16356.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened Focussed refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 435.814 Å		0.85 Å/pix.
x 512 pix.
= 435.814 Å		0.85 Å/pix.
x 512 pix.
= 435.814 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.408
Minimum - Maximum-0.0008219319 - 2.8536406
Average (Standard dev.)0.0005039385 (±0.017980518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.8144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Focused Local refinement half map

Fileemd_16356_half_map_1.map
AnnotationFocused Local refinement half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused Local refinement half map

Fileemd_16356_half_map_2.map
AnnotationFocused Local refinement half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HECT E3 UBR5 forming K48 linked Ubiquitin chains

EntireName: HECT E3 UBR5 forming K48 linked Ubiquitin chains
Components
  • Complex: HECT E3 UBR5 forming K48 linked Ubiquitin chains
    • Protein or peptide: E3 ubiquitin-protein ligase UBR5
    • Protein or peptide: Polyubiquitin-B
    • Protein or peptide: Polyubiquitin-B
  • Ligand: 5-azanylpentan-2-one

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Supramolecule #1: HECT E3 UBR5 forming K48 linked Ubiquitin chains

SupramoleculeName: HECT E3 UBR5 forming K48 linked Ubiquitin chains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 620 KDa

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Macromolecule #1: E3 ubiquitin-protein ligase UBR5

MacromoleculeName: E3 ubiquitin-protein ligase UBR5 / type: protein_or_peptide / ID: 1 / Details: 503 K is mutated to R. 710 L is mutated to D. / Number of copies: 2 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310.266188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSGSGAPMTS IHFVVHPLPG TEDQLNDRLR EVSEKLNKYN LNSHPPLNVL EQATIKQCVV GPNHAAFLLE DGRVCRIGFS VQPDRLELG KPDNNDGSKL NSNSGAGRTS RPGRTSDSPW FLSGSETLGR LAGNTLGSRW SSGVGGSGGG SSGRSSAGAR D SRRQTRVI ...String:
GSGSGAPMTS IHFVVHPLPG TEDQLNDRLR EVSEKLNKYN LNSHPPLNVL EQATIKQCVV GPNHAAFLLE DGRVCRIGFS VQPDRLELG KPDNNDGSKL NSNSGAGRTS RPGRTSDSPW FLSGSETLGR LAGNTLGSRW SSGVGGSGGG SSGRSSAGAR D SRRQTRVI RTGRDRGSGL LGSQPQPVIP ASVIPEELIS QAQVVLQGKS RSVIIRELQR TNLDVNLAVN NLLSRDDEDG DD GDDTASE SYLPGEDLMS LLDADIHSAH PSVIIDADAM FSEDISYFGY PSFRRSSLSR LGSSRVLLLP LERDSELLRE RES VLRLRE RRWLDGASFD NERGSTSKEG EPNLDKKNTP VQSPVSLGED LQWWPDKDGT KFICIGALYS ELLAVSSKGE LYQW KWSES EPYRNAQNPS LHHPRATFLG LTNEKIVLLS ANSIRATVAT ENNKVATWVD ETLSSVASKL EHTAQTYSEL QGERI VSLH CCALYTCAQL ENSLYWWGVV PFSQRRKMLE KARAKNKKPK SSAGISSMPN ITVGTQVCLR NNPLYHAGAV AFSISA GIP KVGVLMESVW NMNDSCRFQL RSPESLKNME KASKTTEAKP ESKQEPVKTE MGPPPSPAST CSDASSIASS ASMPYKR RR STPAPKEEEK VNEEQWSLRE VVFVEDVKNV PVGKVLKVDG AYVAVKFPGT SSNTNCQNSS GPDADPSSLL QDCRDLRI D ELQVVKTGGT PKVPDCFQRT PKKLCIPEKT EILAVNVDSK GVHAVLKTGN WVRYCIFDLA TGKAEQENNF PTSSIAFLG QNERNVAIFT AGQESPIILR DGNGTIYPMA KDCMGGIRDP DWLDLPPISS LGMGVHSLIN LPANSTIKKK AAVIIMAVEK QTLMQHILR CDYEACRQYL MNLEQAVVLE QNLQMLQTFI SHRCDGNRNI LHACVSVCFP TSNKETKEEE EAERSERNTF A ERLSAVEA IANAISVVSS NGPGNRAGSS SSRSLRLREM MRRSLRAAGL GRHEAGASSS DHQDPVSPPI APPSWVPDPP AM DPDGDID FILAPAVGSL TTAATGTGQG PSTSTIPGPS TEPSVVESKD RKANAHFILK LLCDSVVLQP YLRELLSAKD ARG MTPFMS AVSGRAYPAA ITILETAQKI AKAEISSSEK EEDVFMGMVC PSGTNPDDSP LYVLCCNDTC SFTWTGAEHI NQDI FECRT CGLLESLCCC TECARVCHKG HDCKLKRTSP TAYCDCWEKC KCKTLIAGQK SARLDLLYRL LTATNLVTLP NSRGE HLLL FLVQTVARQT VEHCQYRPPR IREDRNRKTA SPEDSDMPDH DLEPPRFAQL ALERVLQDWN ALKSMIMFGS QENKDP LSA SSRIGHLLPE EQVYLNQQSG TIRLDCFTHC LIVKCTADIL LLDTLLGTLV KELQNKYTPG RREEAIAVTM RFLRSVA RV FVILSVEMAS SKKKNNFIPQ PIGKCKRVFQ ALLPYAVEEL CNVAESLIVP VRMGIARPTA PFTLASTSID AMQGSEEL F SVEPLPPRPS SDQSSSSSQS QSSYIIRNPQ QRRISQSQPV RGRDEEQDDI VSADVEEVEV VEGVAGEEDH HDEQEEHGE ENAEAEGQHD EHDEDGSDME LDLLAAAETE SDSESNHSNQ DNASGRRSVV TAATAGSEAG ASSVPAFFSE DDSQSNDSSD SDSSSSQSD DIEQETFMLD EPLERTTNSS HANGAAQAPR SMQWAVRNTQ HQRAASTAPS STSTPAASSA GLIYIDPSNL R RSGTISTS AAAAAAALEA SNASSYLTSA SSLARAYSIV IRQISDLMGL IPKYNHLVYS QIPAAVKLTY QDAVNLQNYV EE KLIPTWN WMVSIMDSTE AQLRYGSALA SAGDPGHPNH PLHASQNSAR RERMTAREEA SLRTLEGRRR ATLLSARQGM MSA RGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT PQLERKRTRE LLELGIDNED SEHE NDDDT NQSATLNDKD DDSLPAETGQ NHPFFRRSDS MTFLGCIPPN PFEVPLAEAI PLADQPHLLQ PNARKEDLFG RPSQG LYSS SASSGKCLME VTVDRNCLEV LPTKMSYAAN LKNVMNMQNR QKKEGEEQPV LPEETESSKP GPSAHDLAAQ LKSSLL AEI GLTESEGPPL TSFRPQCSFM GMVISHDMLL GRWRLSLELF GRVFMEDVGA EPGSILTELG GFEVKESKFR REMEKLR NQ QSRDLSLEVD RDRDLLIQQT MRQLNNHFGR RCATTPMAVH RVKVTFKDEP GEGSGVARSF YTAIAQAFLS NEKLPNLE C IQNANKGTHT SLMQRLRNRG ERDRERERER EMRRSSGLRA GSRRDRDRDF RRQLSIDTRP FRPASEGNPS DDPEPLPAH RQALGERLYP RVQAMQPAFA SKITGMLLEL SPAQLLLLLA SEDSLRARVD EAMELIIAHG RENGADSILD LGLVDSSEKV QQENRKRHG SSRSVVDMDL DDTDDGDDNA PLFYQPGKRG FYTPRPGKNT EARLNCFRNI GRILGLCLLQ NELCPITLNR H VIKVLLGR KVNWHDFAFF DPVMYESLRQ LILASQSSDA DAVFSAMDLA FAIDLCKEEG GGQVELIPNG VNIPVTPQNV YE YVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML ISFTSFNDES GENAEKLLQF KRW FWSIVE KMSMTERQDL VYFWTSSPSL PASEEGFQPM PSITIRPPDD QHLPTANTCI SRLYVPLYSS KQILKQKLLL AIKT KNFGF V

UniProtKB: E3 ubiquitin-protein ligase UBR5

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Macromolecule #2: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 2 / Details: 48 LYS is mutated to CYS in the sequence / 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 DTIENVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

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Macromolecule #3: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 3 / 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-B

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Macromolecule #4: 5-azanylpentan-2-one

MacromoleculeName: 5-azanylpentan-2-one / type: ligand / ID: 4 / Number of copies: 1 / Formula: SY8
Molecular weightTheoretical: 101.147 Da
Chemical component information

ChemComp-SY8:
5-azanylpentan-2-one

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141034
FSC plot (resolution estimation)

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