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- EMDB-17542: Negative stain map of UBR5 (dimer) in complex with RARA/RXRA -

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Basic information

Entry
Database: EMDB / ID: EMD-17542
TitleNegative stain map of UBR5 (dimer) in complex with RARA/RXRA
Map dataHalf-map A.
Sample
  • Complex: UBR5 in complex with RARA/RXRA
    • Protein or peptide: UBR5
    • Protein or peptide: RARA
    • Protein or peptide: RXRA
KeywordsE3 / ubiquitin ligase / HECT / LIGASE
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / heterochromatin boundary formation / glandular epithelial cell development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / growth plate cartilage development / negative regulation of granulocyte differentiation ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / heterochromatin boundary formation / glandular epithelial cell development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / growth plate cartilage development / negative regulation of granulocyte differentiation / protein K29-linked ubiquitination / protein kinase B binding / prostate gland development / positive regulation of T-helper 2 cell differentiation / cytoplasm protein quality control by the ubiquitin-proteasome system / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / negative regulation of cartilage development / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / outflow tract septum morphogenesis / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / protein K11-linked ubiquitination / nuclear vitamin D receptor binding / response to vitamin A / heterocyclic compound binding / apoptotic cell clearance / ureteric bud development / Signaling by Retinoic Acid / regulation of myelination / DNA-binding transcription repressor activity / DNA binding domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / ubiquitin-ubiquitin ligase activity / positive regulation of lipid metabolic process / limb development / DNA repair-dependent chromatin remodeling / LBD domain binding / protein kinase A binding / positive regulation of interleukin-4 production / positive regulation of lipoprotein transport / face development / germ cell development / alpha-actinin binding / negative regulation of type II interferon production / nuclear steroid receptor activity / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / monocyte differentiation / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cellular response to low-density lipoprotein particle stimulus / response to retinoic acid / positive regulation of bone mineralization / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Recycling of bile acids and salts / retinoic acid receptor signaling pathway / protein K48-linked ubiquitination / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to retinoic acid / cell maturation / Regulation of lipid metabolism by PPARalpha / positive regulation of cell cycle / response to cytokine / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / mRNA regulatory element binding translation repressor activity / ubiquitin binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / neural tube closure / Heme signaling / liver development / female pregnancy
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 ...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 / Retinoic acid receptor / 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 / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5 / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 25.0 Å
AuthorsAguirre JD / Cavadini S / Kempf G / Kater L / Thoma NH
Funding support Switzerland, European Union, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation179541 Switzerland
Swiss National Science Foundation201206 Switzerland
European Research Council (ERC)884331European Union
CitationJournal: Mol Cell / Year: 2023
Title: UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability.
Authors: Jonathan M Tsai / Jacob D Aguirre / Yen-Der Li / Jared Brown / Vivian Focht / Lukas Kater / Georg Kempf / Brittany Sandoval / Stefan Schmitt / Justine C Rutter / Pius Galli / Colby R Sandate ...Authors: Jonathan M Tsai / Jacob D Aguirre / Yen-Der Li / Jared Brown / Vivian Focht / Lukas Kater / Georg Kempf / Brittany Sandoval / Stefan Schmitt / Justine C Rutter / Pius Galli / Colby R Sandate / Jevon A Cutler / Charles Zou / Katherine A Donovan / Ryan J Lumpkin / Simone Cavadini / Paul M C Park / Quinlan Sievers / Charlie Hatton / Elizabeth Ener / Brandon D Regalado / Micah T Sperling / Mikołaj Słabicki / Jeonghyeon Kim / Rebecca Zon / Zinan Zhang / Peter G Miller / Roger Belizaire / Adam S Sperling / Eric S Fischer / Rafael Irizarry / Scott A Armstrong / Nicolas H Thomä / Benjamin L Ebert /
Abstract: Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand- ...Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.
History
DepositionMay 31, 2023-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17542.png

Downloads & links

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Map

FileDownload / File: emd_17542.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf-map A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 256 pix.
= 563.2 Å		2.2 Å/pix.
x 256 pix.
= 563.2 Å		2.2 Å/pix.
x 256 pix.
= 563.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.9
Minimum - Maximum-0.4285514 - 3.2889066
Average (Standard dev.)-0.005750237 (±0.18206154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Full-map.

Fileemd_17542_half_map_1.map
AnnotationFull-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B.

Fileemd_17542_half_map_2.map
AnnotationHalf-map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UBR5 in complex with RARA/RXRA

EntireName: UBR5 in complex with RARA/RXRA
Components
  • Complex: UBR5 in complex with RARA/RXRA
    • Protein or peptide: UBR5
    • Protein or peptide: RARA
    • Protein or peptide: RXRA

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Supramolecule #1: UBR5 in complex with RARA/RXRA

SupramoleculeName: UBR5 in complex with RARA/RXRA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: UBR5

MacromoleculeName: UBR5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKL AAANSSIDLI STSLYKKAGF RTMTSIHFVV HPLPGTEDQL NDRLREVSEK LNKYNLNSHP PLNVLEQATI KQCVVGPNHA AFLLEDGRVC RIGFSVQPDR LELGKPDNND GSKLNSNSGA GRTSRPGRTS DSPWFLSGSE TLGRLAGNTL GSRWSSGVGG ...String:
MDYKDDDDKL AAANSSIDLI STSLYKKAGF RTMTSIHFVV HPLPGTEDQL NDRLREVSEK LNKYNLNSHP PLNVLEQATI KQCVVGPNHA AFLLEDGRVC RIGFSVQPDR LELGKPDNND GSKLNSNSGA GRTSRPGRTS DSPWFLSGSE TLGRLAGNTL GSRWSSGVGG SGGGSSGRSS AGARDSRRQT RVIRTGRDRG SGLLGSQPQP VIPASVIPEE LISQAQVVLQ GKSRSVIIRE LQRTNLDVNL AVNNLLSRDD EDGDDGDDTA SESYLPGEDL MSLLDADIHS AHPSVIIDAD AMFSEDISYF GYPSFRRSSL SRLGSSRVLL LPLERDSELL RERESVLRLR ERRWLDGASF DNERGSTSKE GEPNLDKKNT PVQSPVSLGE DLQWWPDKDG TKFICIGALY SELLAVSSKG ELYQWKWSES EPYRNAQNPS LHHPRATFLG LTNEKIVLLS ANSIRATVAT ENNKVATWVD ETLSSVASKL EHTAQTYSEL QGERIVSLHC CALYTCAQLE NSLYWWGVVP FSQRRKMLEK ARAKNKKPKS SAGKTGGTPK VPDCFQRTPK KLCIPEKTEI LAVNVDSKGV HAVLKTGNWV RYCIFDLATG KAEQENNFPT SSIAFLGQNE RNVAIFTAGQ ESPIILRDGN GTIYPMAKDC MGGIRDPDWL DLPPISSLGM GVHSLINLPA NSTIKKKAAV IIMAVEKQTL MQHILRCDYE ACRQYLMNLE QAVVLEQNLQ MLQTFISHRC DGNRNILHAC VSVCFPTSNK ETKEEEEAER SERNTFAERL SAVEAIANAI SVVSSNGPGN RAGSSSSRSL RLREMMRRSL RAAGLGRHEA GASSSDHQDP VSPPIAPPSW VPDPPAMDPD GDIDFILAPA VGSLTTAATG TGQGPSTSTI PGPSTEPSVV ESKDRKANAH FILKLLCDSV VLQPYLRELL SAKDARGMTP FMSAVSGRAY PAAITILETA QKIAKAEISS SEKEEDVFMG MVCPSGTNPD DSPLYVLCCN DTCSFTWTGA EHINQDIFEC RTCGLLESLC CCTECARVCH KGHDCKLKRT SPTAYCDCWE KCKCKTLIAG QKSARLDLLY RLLTATNLVT LPNSRGEHLL LFLVQTVARQ TVEHCQYRPP RIREDRNRKT ASPEDSDMPD HDLEPPRFAQ LALERVLQDW NALKSMIMFG SQENKDPLSA SSRIGHLLPE EQVYLNQQSG TIRLDCFTHC LIVKCTADIL LLDTLLGTLV KELQNKYTPG RREEAIAVTM RFLRSVARVF VILSVEMASS KKKNNFIPQP IGKCKRVFQA LLPYAVEELC NVAESLIVPV RMGIARPTAP FTLASTSIDA MQGSEELFSV EPLPPRPSSD QSSSSSQSQS SYIIRNPQQR RISQSQPVRG RDEEQDDIVS ADVEEVEVVE GVAGEEDHHD EQEEHGEENA EAEGQHDEHD EDGSDMELDL LAAAETESDS ESNHSNQDNA SGRRSVVTAA TAGSEAGASS VPAFFSEDDS QSNDSSDSDS SSSQSDDIEQ ETFMLDEPLE RTTNSSHANG AAQAPRSMQW AVRNTQHQRA ASTAPSSTST PAASSAGLIY IDPSNLRRSG TISTSAAAAA AALEASNASS YLTSASSLAR AYSIVIRQIS DLMGLIPKYN HLVYSQIPAA VKLTYQDAVN LQNYVEEKLI PTWNWMVSIM DSTEAQLRYG SALASAGDPG HPNHPLHASQ NSARRERMTA REEASLRTLE GRRRATLLSA RQGMMSARGD FLNYALSLMR SHNDEHSDVL PVLDVCSLKH VAYVFQALIY WIKAMNQQTT LDTPQLERKR TRELLELGID NEDSEHENDD DTNQSATLND KDDDSLPAET GQNHPFFRRS DSMTFLGCIP PNPFEVPLAE AIPLADQPHL LQPNARKEDL FGRPSQGLYS SSASSGKCLM EVTVDRNCLE VLPTKMSYAA NLKNVMNMQN RQKKEGEEQP VLPEETESSK PGPSAHDLAA QLKSSLLAEI GLTESEGPPL TSFRPQCSFM GMVISHDMLL GRWRLSLELF GRVFMEDVGA EPGSILTELG G

UniProtKB: E3 ubiquitin-protein ligase UBR5

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Macromolecule #2: RARA

MacromoleculeName: RARA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSHHHHHHH HHHSGMSDSE VNQEAKPEVK PEVKPETHIN LKVSDGSSEI FFKIKKTTPL RRLMEAFAKR QGKEMDSLTF LYDGIEIQAD QTPEDLDMED NDIIEAHREQ IGGDENLYFQ SESYTLTPEV GELIEKVRKA HQETFPALCQ LGKYTTNNSS EQRVSLDIDL ...String:
MDSHHHHHHH HHHSGMSDSE VNQEAKPEVK PEVKPETHIN LKVSDGSSEI FFKIKKTTPL RRLMEAFAKR QGKEMDSLTF LYDGIEIQAD QTPEDLDMED NDIIEAHREQ IGGDENLYFQ SESYTLTPEV GELIEKVRKA HQETFPALCQ LGKYTTNNSS EQRVSLDIDL WDKFSELSTK CIIKTVEFAK QLPGFTTLTI ADQITLLKAA CLDILILRIC TRYTPEQDTM TFSDGLTLNR TQMHNAGFGP LTDLVFAFAN QLLPLEMDDA ETGLLSAICL ICGDRQDLEQ PDRVDMLQEP LLEALKVYVR KRRPSRPHMF PKMLMKITDL RSISAKGAER VITLKMEIPG SMPPLIQEML ENSEGLD

UniProtKB: Retinoic acid receptor alpha

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Macromolecule #3: RXRA

MacromoleculeName: RXRA / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDSHHHHHHH HHHSGMSDSE VNQEAKPEVK PEVKPETHIN LKVSDGSSEI FFKIKKTTPL RRLMEAFAKR QGKEMDSLTF LYDGIEIQAD QTPEDLDMED NDIIEAHREQ IGGDENLYFQ SANEDMPVER ILEAELAVEP KTETYVEANM GLNPSSPNDP VTNICQAADK ...String:
MDSHHHHHHH HHHSGMSDSE VNQEAKPEVK PEVKPETHIN LKVSDGSSEI FFKIKKTTPL RRLMEAFAKR QGKEMDSLTF LYDGIEIQAD QTPEDLDMED NDIIEAHREQ IGGDENLYFQ SANEDMPVER ILEAELAVEP KTETYVEANM GLNPSSPNDP VTNICQAADK QLFTLVEWAK RIPHFSELPL DDQVILLRAG WNELLIASFS HRSIAVKDGI LLATGLHVHR NSAHSAGVGA IFDRVLTELV SKMRDMQMDK TELGCLRAIV LFNPDSKGLS NPAEVEALRE KVYASLEAYC KHKYPEQPGR FAKLLLRLPA LRSIGLKCLE HLFFFKLIGD TPIDTFLMEM LEAPHQMT

UniProtKB: Retinoic acid receptor RXR-alpha

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 500.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 6389
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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