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- EMDB-16355: Structure of Dimeric HECT E3 Ubiquitin Ligase UBR5 -

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Basic information

Entry
Database: EMDB / ID: EMD-16355
TitleStructure of Dimeric HECT E3 Ubiquitin Ligase UBR5
Map data
Sample
  • Complex: Dimeric HECT E3 Ubiquitin Ligase UBR5
    • Protein or peptide: E3 ubiquitin-protein ligase UBR5
  • Ligand: ZINC ION
KeywordsE3 ligase / UBR5 / Ubiquitination / UBQ / Ubiquitin / HECT / LIGASE
Function / homology
Function and homology information


heterochromatin boundary formation / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / nuclear protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / protein K11-linked ubiquitination / ubiquitin-ubiquitin ligase activity / DNA repair-dependent chromatin remodeling ...heterochromatin boundary formation / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / nuclear protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / protein K11-linked ubiquitination / ubiquitin-ubiquitin ligase activity / DNA repair-dependent chromatin remodeling / protein K48-linked ubiquitination / progesterone receptor signaling pathway / ubiquitin binding / negative regulation of smoothened signaling pathway / positive regulation of protein import into nucleus / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / DNA damage response / positive regulation of gene expression / chromatin / perinuclear region of cytoplasm / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
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. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE domain / Zinc finger, UBR-type / Zinc finger UBR-type profile. ...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. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / MLLE 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_16355.png

Downloads & links

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Map

FileDownload / File: emd_16355.map.gz / Format: CCP4 / Size: 216 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.)
0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0101
Minimum - Maximum-0.04995323 - 0.09133466
Average (Standard dev.)0.00013561577 (±0.0014846632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.86078 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16355_msk_1.map
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Additional map: #1

Fileemd_16355_additional_1.map
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Half map: #2

Fileemd_16355_half_map_1.map
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Half map: #1

Fileemd_16355_half_map_2.map
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Sample components

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Entire : Dimeric HECT E3 Ubiquitin Ligase UBR5

EntireName: Dimeric HECT E3 Ubiquitin Ligase UBR5
Components
  • Complex: Dimeric HECT E3 Ubiquitin Ligase UBR5
    • Protein or peptide: E3 ubiquitin-protein ligase UBR5
  • Ligand: ZINC ION

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Supramolecule #1: Dimeric HECT E3 Ubiquitin Ligase UBR5

SupramoleculeName: Dimeric HECT E3 Ubiquitin Ligase UBR5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 / Number of copies: 6 / 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: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 6 / 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: 67.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 226919
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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