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

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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 / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / nuclear protein quality control by the ubiquitin-proteasome system / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...heterochromatin boundary formation / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / nuclear protein quality control by the ubiquitin-proteasome system / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / ubiquitin-ubiquitin ligase activity / mitochondrion transport along microtubule / fat pad development / DNA repair-dependent chromatin remodeling / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process / protein K48-linked ubiquitination / progesterone receptor signaling pathway / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling
Similarity search - Function
E3 ubiquitin ligase EDD, ubiquitin-associated domain / : / E3 ubiquitin ligase EDD / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain ...E3 ubiquitin ligase EDD, ubiquitin-associated domain / : / E3 ubiquitin ligase EDD / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / 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 domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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-
UpdateOct 9, 2024-
Current statusOct 9, 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
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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 141034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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