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- EMDB-17541: Cryo-EM density map of UBR5 in complex with MCRS1 -

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Basic information

Entry
Database: EMDB / ID: EMD-17541
TitleCryo-EM density map of UBR5 in complex with MCRS1
Map dataAmplitude-scaled map (LocScale).
Sample
  • Complex: UBR5 in complex with MCRS1
    • Protein or peptide: UBR5
    • Protein or peptide: MCRS1
KeywordsE3 / ubiquitin ligase / HECT / orphan substrate / LIGASE
Function / homology
Function and homology information


: / heterochromatin boundary formation / poly(G) binding / positive regulation of protein localization to nucleolus / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / telomerase inhibitor activity / protein K29-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / nuclear protein quality control by the ubiquitin-proteasome system ...: / heterochromatin boundary formation / poly(G) binding / positive regulation of protein localization to nucleolus / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / telomerase inhibitor activity / 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 / Ino80 complex / HECT-type E3 ubiquitin transferase / cytoplasm protein quality control / NSL complex / protein K11-linked ubiquitination / negative regulation of telomere maintenance via telomere lengthening / poly(U) RNA binding / ubiquitin-ubiquitin ligase activity / regulation of chromosome organization / DNA repair-dependent chromatin remodeling / Formation of WDR5-containing histone-modifying complexes / regulation of DNA replication / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / regulation of DNA repair / protein K48-linked ubiquitination / progesterone receptor signaling pathway / telomere maintenance / positive regulation of DNA repair / ubiquitin binding / negative regulation of smoothened signaling pathway / DNA Damage Recognition in GG-NER / protein modification process / positive regulation of protein import into nucleus / protein polyubiquitination / UCH proteinases / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / HATs acetylate histones / G-quadruplex RNA binding / DNA recombination / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of cell cycle / chromatin remodeling / DNA repair / dendrite / DNA damage response / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Microspherule protein 1 / Microspherule protein, N-terminal domain / N-terminal region of micro-spherule protein / 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 ...Microspherule protein 1 / Microspherule protein, N-terminal domain / N-terminal region of micro-spherule protein / 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 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR5 / Microspherule protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 Å
AuthorsSchmitt S / Aguirre JD / 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: Cell / Year: 2023
Title: Orphan quality control shapes network dynamics and gene expression.
Authors: Kevin G Mark / SriDurgaDevi Kolla / Jacob D Aguirre / Danielle M Garshott / Stefan Schmitt / Diane L Haakonsen / Christina Xu / Lukas Kater / Georg Kempf / Brenda Martínez-González / David ...Authors: Kevin G Mark / SriDurgaDevi Kolla / Jacob D Aguirre / Danielle M Garshott / Stefan Schmitt / Diane L Haakonsen / Christina Xu / Lukas Kater / Georg Kempf / Brenda Martínez-González / David Akopian / Stephanie K See / Nicolas H Thomä / Michael Rapé /
Abstract: All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in ...All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.
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_17541.png

Downloads & links

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Map

FileDownload / File: emd_17541.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAmplitude-scaled map (LocScale).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 256 pix.
= 432.64 Å		1.69 Å/pix.
x 256 pix.
= 432.64 Å		1.69 Å/pix.
x 256 pix.
= 432.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0455
Minimum - Maximum-0.10708313 - 0.2361024
Average (Standard dev.)0.0011925799 (±0.009012154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 432.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map.

Fileemd_17541_additional_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 A.

Fileemd_17541_half_map_1.map
AnnotationHalf-map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B.

Fileemd_17541_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 MCRS1

EntireName: UBR5 in complex with MCRS1
Components
  • Complex: UBR5 in complex with MCRS1
    • Protein or peptide: UBR5
    • Protein or peptide: MCRS1

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Supramolecule #1: UBR5 in complex with MCRS1

SupramoleculeName: UBR5 in complex with MCRS1 / 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: DYKDDDDKLA AANSSIDLIS TSLYKKAGFR TMTSIHFVVH PLPGTEDQLN DRLREVSEKL NKYNLNSHPP LNVLEQATIK QCVVGPNHAA FLLEDGRVCR IGFSVQPDRL ELGKPDNNDG SKLNSNSGAG RTSRPGRTSD SPWFLSGSET LGRLAGNTLG SRWSSGVGGS ...String:
DYKDDDDKLA AANSSIDLIS TSLYKKAGFR TMTSIHFVVH PLPGTEDQLN DRLREVSEKL NKYNLNSHPP LNVLEQATIK QCVVGPNHAA FLLEDGRVCR IGFSVQPDRL ELGKPDNNDG SKLNSNSGAG RTSRPGRTSD SPWFLSGSET LGRLAGNTLG SRWSSGVGGS GGGSSGRSSA GARDSRRQTR VIRTGRDRGS GLLGSQPQPV IPASVIPEEL ISQAQVVLQG KSRSVIIREL QRTNLDVNLA VNNLLSRDDE DGDDGDDTAS ESYLPGEDLM SLLDADIHSA HPSVIIDADA MFSEDISYFG YPSFRRSSLS RLGSSRVLLL PLERDSELLR ERESVLRLRE RRWLDGASFD NERGSTSKEG EPNLDKKNTP VQSPVSLGED LQWWPDKDGT KFICIGALYS ELLAVSSKGE LYQWKWSESE PYRNAQNPSL HHPRATFLGL TNEKIVLLSA NSIRATVATE NNKVATWVDE TLSSVASKLE HTAQTYSELQ GERIVSLHCC ALYTCAQLEN SLYWWGVVPF SQRRKMLEKA RAKNKKPKSS AGISSMPNIT VGTQVCLRNN PLYHAGAVAF SISAGIPKVG VLMESVWNMN DSCRFQLRSP ESLKNMEKAS KTTEAKPESK QEPVKTEMGP PPSPASTCSD ASSIASSASM PYKRRRSTPA PKEEEKVNEE QWSLREVVFV EDVKNVPVGK VLKVDGAYVA VKFPGTSSNT NCQNSSGPDA DPSSLLQDCR LLRIDELQVV KTGGTPKVPD CFQRTPKKLC IPEKTEILAV NVDSKGVHAV LKTGNWVRYC IFDLATGKAE QENNFPTSSI AFLGQNERNV AIFTAGQESP IILRDGNGTI YPMAKDCMGG IRDPDWLDLP PISSLGMGVH SLINLPANST IKKKAAVIIM AVEKQTLMQH ILRCDYEACR QYLMNLEQAV VLEQNLQMLQ TFISHRCDGN RNILHACVSV CFPTSNKETK EEEEAERSER NTFAERLSAV EAIANAISVV SSNGPGNRAG SSSSRSLRLR EMMRRSLRAA GLGRHEAGAS SSDHQDPVSP PIAPPSWVPD PPAMDPDGDI DFILAPAVGS LTTAATGTGQ GPSTSTIPGP STEPSVVESK DRKANAHFIL KLLCDSVVLQ PYLRELLSAK DARGMTPFMS AVSGRAYPAA ITILETAQKI AKAEISSSEK EEDVFMGMVC PSGTNPDDSP LYVLCCNDTC SFTWTGAEHI NQDIFECRTC GLLESLCCCT ECARVCHKGH DCKLKRTSPT AYCDCWEKCK CKTLIAGQKS ARLDLLYRLL TATNLVTLPN SRGEHLLLFL VQTVARQTVE HCQYRPPRIR EDRNRKTASP EDSDMPDHDL EPPRFAQLAL ERVLQDWNAL KSMIMFGSQE NKDPLSASSR IGHLLPEEQV YLNQQSGTIR LDCFTHCLIV KCTADILLLD TLLGTLVKEL QNKYTPGRRE EAIAVTMRFL RSVARVFVIL SVEMASSKKK NNFIPQPIGK CKRVFQALLP YAVEELCNVA ESLIVPVRMG IARPTAPFTL ASTSIDAMQG SEELFSVEPL PPRPSSDQSS SSSQSQSSYI IRNPQQRRIS QSQPVRGRDE EQDDIVSADV EEVEVVEGVA GEEDHHDEQE EHGEENAEAE GQHDEHDEDG SDMELDLLAA AETESDSESN HSNQDNASGR RSVVTAATAG SEAGASSVPA FFSEDDSQSN DSSDSDSSSS QSDDIEQETF MLDEPLERTT NSSHANGAAQ APRSMQWAVR NTQHQRAAST APSSTSTPAA SSAGLIYIDP SNLRRSGTIS TSAAAAAAAL EASNASSYLT SASSLARAYS IVIRQISDLM GLIPKYNHLV YSQIPAAVKL TYQDAVNLQN YVEEKLIPTW NWMVSIMDST EAQLRYGSAL ASAGDPGHPN HPLHASQNSA RRERMTAREE ASLRTLEGRR RATLLSARQG MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT PQLERKRTRE LLELGIDNED SEHENDDDTN QSATLNDKDD DSLPAETGQN HPFFRRSDSM TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA SSGKCLMEVT VDRNCLEVLP TKMSYAANLK NVMNMQNRQK KEGEEQPVLP EETESSKPGP SAHDLAAQLK SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLECIQNAN KGTHTSLMQR LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPEP LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVDEAMELI IAHGRENGAD SILDLGLVDS SEKVQQENRK RHGSSRSVVD MDLDDTDDGD DNAPLFYQPG KRGFYTPRPG KNTEARLNCF RNIGRILGLC LLQNELCPIT LNRHVIKVLL GRKVNWHDFA FFDPVMYESL RQLILASQSS DADAVFSAMD LAFAIDLCKE EGGGQVELIP NGVNIPVTPQ NVYEYVRKYA EHRMLVVAEQ PLHAMRKGLL DVLPKNSLED LTAEDFRLLV NGCGEVNVQM LISFTSFNDE SGENAEKLLQ FKRWFWSIVE KMSMTERQDL VYFWTSSPSL PASEEGFQPM PSITIRPPDD QHLPTANTCI SRLYVPLYSS KQILKQKLLL AIKTKNFGFV

UniProtKB: E3 ubiquitin-protein ligase UBR5

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Macromolecule #2: MCRS1

MacromoleculeName: MCRS1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK GGGSGGSGGG SSAWSHPQFE KSAMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLTFLY DGIEIQADQT PEDLDMEDND IIEAHREQIG GENLYFQGGR DSQGLLDSSL MASGTASRSE DEESLAGQKR ...String:
MDWSHPQFEK GGGSGGSGGG SSAWSHPQFE KSAMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLTFLY DGIEIQADQT PEDLDMEDND IIEAHREQIG GENLYFQGGR DSQGLLDSSL MASGTASRSE DEESLAGQKR ASSQALGTIP KRRSSSRFIK RKKFDDELVE SSLAKSSTRA KGASGVEPGR CSGSEPSSSE KKKVSKAPST PVPPSPAPAP GLTKRVKKSK QPLQVTKDLG RWKPADDLLL INAVLQTNDL TSVHLGVKFS CRFTLREVQE RWYALLYDPV ISKLACQAMR QLHPEAIAAI QSKALFSKAE EQLLSKVGST SQPTLETFQD LLHRHPDAFY LARTAKALQA HWQLMKQYYL LEDQTVQPLP KGDQVLNFSD AEDLIDDSKL KDMRDEVLEH ELMVADRRQK REIRQLEQEL HKWQVLVDSI TGMSSPDFDN QTLAVLRGRM VRYLMRSREI TLGRATKDNQ IDVDLSLEGP AWKISRKQGV IKLKNNGDFF IANEGRRPIY IDGRPVLCGS KWRLSNNSVV EIASLRFVFL INQDLIALIR AEAAKITPQ

UniProtKB: Microspherule protein 1

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26647
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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