+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16087 | |||||||||
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Title | Structure of the human UBR5 Dimer. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | UBR5 / E3 Ligase / nuclear / Degradation / Ubiquitin / LIGASE | |||||||||
Function / homology | Function and homology information heterochromatin boundary formation / cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / 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 / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity ...heterochromatin boundary formation / cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / 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 / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / protein K48-linked ubiquitination / progesterone receptor signaling pathway / negative regulation of smoothened signaling pathway / ubiquitin binding / 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 / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Hodakova Z / Grishkovskaya I / Haselbach D | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: EMBO J / Year: 2023 Title: Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. Authors: Zuzana Hodáková / Irina Grishkovskaya / Hanna L Brunner / Derek L Bolhuis / Katarina Belačić / Alexander Schleiffer / Harald Kotisch / Nicholas G Brown / David Haselbach / Abstract: UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important ...UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16087.map.gz | 54.2 MB | EMDB map data format | |
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Header (meta data) | emd-16087-v30.xml emd-16087.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
Images | emd_16087.png | 49.6 KB | ||
Others | emd_16087_additional_1.map.gz emd_16087_additional_2.map.gz emd_16087_half_map_1.map.gz emd_16087_half_map_2.map.gz | 86.9 MB 165.1 MB 58.7 MB 58.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16087 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16087 | HTTPS FTP |
-Validation report
Summary document | emd_16087_validation.pdf.gz | 739.2 KB | Display | EMDB validaton report |
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Full document | emd_16087_full_validation.pdf.gz | 738.8 KB | Display | |
Data in XML | emd_16087_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_16087_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16087 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16087 | HTTPS FTP |
-Related structure data
Related structure data | 8bjaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16087.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.489 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_16087_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map of UBR5 tetramer
File | emd_16087_additional_2.map | ||||||||||||
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Annotation | Map of UBR5 tetramer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16087_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16087_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : UBR5
Entire | Name: UBR5 |
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Components |
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-Supramolecule #1: UBR5
Supramolecule | Name: UBR5 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homodimer |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 310 kDa/nm |
-Macromolecule #1: E3 ubiquitin-protein ligase UBR5
Macromolecule | Name: E3 ubiquitin-protein ligase UBR5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 312.810906 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTSIHFVVHP LPGTEDQLND RLREVSEKLN KYNLNSHPPL NVLEQATIKQ CVVGPNHAAF LLEDGRVCRI GFSVQPDRLE LGKPDNNDG SKLNSNSGAG RTSRPGRTSD SPWFLSGSET LGRLAGNTLG SRWSSGVGGS GGGSSGRSSA GARDSRRQTR V IRTGRDRG ...String: MTSIHFVVHP LPGTEDQLND RLREVSEKLN KYNLNSHPPL NVLEQATIKQ CVVGPNHAAF LLEDGRVCRI GFSVQPDRLE LGKPDNNDG SKLNSNSGAG RTSRPGRTSD SPWFLSGSET LGRLAGNTLG SRWSSGVGGS GGGSSGRSSA GARDSRRQTR V IRTGRDRG SGLLGSQPQP VIPASVIPEE LISQAQVVLQ GKSRSVIIRE LQRTNLDVNL AVNNLLSRDD EDGDDGDDTA SE SYLPGED LMSLLDADIH SAHPSVIIDA DAMFSEDISY FGYPSFRRSS LSRLGSSRVL LLPLERDSEL LRERESVLRL RER RWLDGA SFDNERGSTS KEGEPNLDKK NTPVQSPVSL GEDLQWWPDK DGTKFICIGA LYSELLAVSS KGELYQWKWS ESEP YRNAQ NPSLHHPRAT FLGLTNEKIV LLSANSIRAT VATENNKVAT WVDETLSSVA SKLEHTAQTY SELQGERIVS LHCCA LYTC AQLENSLYWW GVVPFSQRKK MLEKARAKNK KPKSSAGISS MPNITVGTQV CLRNNPLYHA GAVAFSISAG IPKVGV LME SVWNMNDSCR FQLRSPESLK NMEKASKTTE AKPESKQEPV KTEMGPPPSP ASTCSDASSI ASSASMPYKR RRSTPAP KE EEKVNEEQWS LREVVFVEDV KNVPVGKVLK VDGAYVAVKF PGTSSNTNCQ NSSGPDADPS SLLQDCRLLR IDELQVVK T GGTPKVPDCF QRTPKKLCIP EKTEILAVNV DSKGVHAVLK TGNWVRYCIF DLATGKAEQE NNFPTSSIAF LGQNERNVA IFTAGQESPI ILRDGNGTIY PMAKDCMGGI RDPDWLDLPP ISSLGMGVHS LINLPANSTI KKKAAVIIMA VEKQTLMQHI LRCDYEACR QYLMNLEQAV VLEQNLQMLQ TFISHRCDGN RNILHACVSV CFPTSNKETK EEEEAERSER NTFAERLSAV E AIANAISV VSSNGPGNRA GSSSSRSLRL REMMRRSLRA AGLGRHEAGA SSSDHQDPVS PPIAPPSWVP DPPAMDPDGD ID FILAPAV GSLTTAATGT GQGPSTSTIP GPSTEPSVVE SKDRKANAHF ILKLLCDSVV LQPYLRELLS AKDARGMTPF MSA VSGRAY PAAITILETA QKIAKAEISS SEKEEDVFMG MVCPSGTNPD DSPLYVLCCN DTCSFTWTGA EHINQDIFEC RTCG LLESL CCCTECARVC HKGHDCKLKR TSPTAYCDCW EKCKCKTLIA GQKSARLDLL YRLLTATNLV TLPNSRGEHL LLFLV QTVA RQTVEHCQYR PPRIREDRNR KTASPEDSDM PDHDLEPPRF AQLALERVLQ DWNALKSMIM FGSQENKDPL SASSRI GHL LPEEQVYLNQ QSGTIRLDCF THCLIVKCTA DILLLDTLLG TLVKELQNKY TPGRREEAIA VTMRFLRSVA RVFVILS VE MASSKKKNNF IPQPIGKCKR VFQALLPYAV EELCNVAESL IVPVRMGIAR PTAPFTLAST SIDAMQGSEE LFSVEPLP P RPSSDQSSSS SQSQSSYIIR NPQQRRISQS QPVRGRDEEQ DDIVSADVEE VEVVEGVAGE EDHHDEQEEH GEENAEAEG QHDEHDEDGS DMELDLLAAA ETESDSESNH SNQDNASGRR SVVTAATAGS EAGASSVPAF FSEDDSQSND SSDSDSSSSQ SDDIEQETF MLDEPLERTT NSSHANGAAQ APRSMQWAVR NTQHQRAAST APSSTSTPAA SSAGLIYIDP SNLRRSGTIS T SAAAAAAA LEASNASSYL TSASSLARAY SIVIRQISDL MGLIPKYNHL VYSQIPAAVK LTYQDAVNLQ NYVEEKLIPT WN WMVSIMD STEAQLRYGS ALASAGDPGH PNHPLHASQN SARRERMTAR EEASLRTLEG RRRATLLSAR QGMMSARGDF LNY ALSLMR SHNDEHSDVL PVLDVCSLKH VAYVFQALIY WIKAMNQQTT LDTPQLERKR TRELLELGID NEDSEHENDD DTNQ SATLN DKDDDSLPAE TGQNHPFFRR SDSMTFLGCI PPNPFEVPLA EAIPLADQPH LLQPNARKED LFGRPSQGLY SSSAS SGKC LMEVTVDRNC LEVLPTKMSY AANLKNVMNM QNRQKKEGEE QPVLPEETES SKPGPSAHDL AAQLKSSLLA EIGLTE SEG PPLTSFRPQC SFMGMVISHD MLLGRWRLSL ELFGRVFMED VGAEPGSILT ELGGFEVKES KFRREMEKLR NQQSRDL SL EVDRDRDLLI QQTMRQLNNH FGRRCATTPM AVHRVKVTFK DEPGEGSGVA RSFYTAIAQA FLSNEKLPNL ECIQNANK G THTSLMQRLR NRGERDRERE REREMRRSSG LRAGSRRDRD RDFRRQLSID TRPFRPASEG NPSDDPEPLP AHRQALGER LYPRVQAMQP AFASKITGML LELSPAQLLL LLASEDSLRA RVDEAMELII AHGRENGADS ILDLGLVDSS EKVQQENRKR HGSSRSVVD MDLDDTDDGD DNAPLFYQPG KRGFYTPRPG KNTEARLNCF RNIGRILGLC LLQNELCPIT LNRHVIKVLL G RKVNWHDF AFFDPVMYES LRQLILASQS SDADAVFSAM DLAFAIDLCK EEGGGQVELI PNGVNIPVTP QNVYEYVRKY AE HRMLVVA EQPLHAMRKG LLDVLPKNSL EDLTAEDFRL LVNGCGEVNV QMLISFTSFN DESGENAEKL LQFKRWFWSI VEK MSMTER QDLVYFWTSS PSLPASEEGF QPMPSITIRP PDDQHLPTAN TCISRLYVPL YSSKQILKQK LLLAIKTKNF GFVG SAWSH PQFEKGGGSG GGSGGSAWSH PQFEK UniProtKB: E3 ubiquitin-protein ligase UBR5 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Sugar embedding | Material: CHAPSO, fOG Details: Sample vitrified using a final concentration of 4mM CHAPSO or 0.005% fluorinated octyl beta-maltoside |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 288287 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Overall B value: 104 |
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Output model | PDB-8bja: |