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- EMDB-16087: Structure of the human UBR5 Dimer. -

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Basic information

Entry
Database: EMDB / ID: EMD-16087
TitleStructure of the human UBR5 Dimer.
Map data
Sample
  • Organelle or cellular component: UBR5
    • Protein or peptide: E3 ubiquitin-protein ligase UBR5
  • Ligand: ZINC ION
KeywordsUBR5 / E3 Ligase / nuclear / Degradation / Ubiquitin / LIGASE
Function / homology
Function and homology information


heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / protein polyubiquitination / positive regulation of protein import into nucleus / positive regulation of canonical Wnt signaling pathway ...heterochromatin boundary formation / HECT-type E3 ubiquitin transferase / DNA repair-dependent chromatin remodeling / ubiquitin-ubiquitin ligase activity / progesterone receptor signaling pathway / protein K48-linked ubiquitination / ubiquitin binding / protein polyubiquitination / positive regulation of protein import into nucleus / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / DNA repair / DNA damage response / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHodakova Z / Grishkovskaya I / Haselbach D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: 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
DepositionNov 3, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16087.png

Downloads & links

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Map

FileDownload / File: emd_16087.map.gz / Format: CCP4 / Size: 103 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.)
1.49 Å/pix.
x 300 pix.
= 446.7 Å		1.49 Å/pix.
x 300 pix.
= 446.7 Å		1.49 Å/pix.
x 300 pix.
= 446.7 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.489 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0632
Minimum - Maximum-0.018491998 - 1.3302218
Average (Standard dev.)0.0005496162 (±0.012445254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 446.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16087_additional_1.map
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Additional map: Map of UBR5 tetramer

Fileemd_16087_additional_2.map
AnnotationMap of UBR5 tetramer
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Half map: #2

Fileemd_16087_half_map_1.map
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Half map: #1

Fileemd_16087_half_map_2.map
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Sample components

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Entire : UBR5

EntireName: UBR5
Components
  • Organelle or cellular component: UBR5
    • Protein or peptide: E3 ubiquitin-protein ligase UBR5
  • Ligand: ZINC ION

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Supramolecule #1: UBR5

SupramoleculeName: UBR5 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homodimer
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310 kDa/nm

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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: 2 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 312.810906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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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
Sugar embeddingMaterial: CHAPSO, fOG
Details: Sample vitrified using a final concentration of 4mM CHAPSO or 0.005% fluorinated octyl beta-maltoside
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 288287

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 104
Output model

PDB-8bja:
Structure of the human UBR5 Dimer.

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