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- EMDB-23806: Structure of yeast Ubr1 in complex with Ubc2 and N-degron -

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Entry
Database: EMDB / ID: EMD-23806
TitleStructure of yeast Ubr1 in complex with Ubc2 and N-degron
Map data
Sample
  • Complex: yeast Ubr1 in complex with Ubc2 and N-degron
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 2
    • Protein or peptide: N-degron
    • Protein or peptide: E3 ubiquitin-protein ligase UBR1
  • Ligand: ZINC ION
KeywordsUbiquitin E3 ligase / ubiquitination / Ubr1 / Ubc2 / Degron / N-end rule / TRANSFERASE
Function / homology
Function and homology information


MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / sno(s)RNA transcription / HULC complex / error-free postreplication DNA repair / proteasome regulatory particle binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / sno(s)RNA transcription / HULC complex / error-free postreplication DNA repair / proteasome regulatory particle binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / meiotic DNA double-strand break formation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / stress-induced homeostatically regulated protein degradation pathway / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / E3 ubiquitin ligases ubiquitinate target proteins / telomere maintenance via recombination / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / DNA duplex unwinding / E2 ubiquitin-conjugating enzyme / sporulation resulting in formation of a cellular spore / error-free translesion synthesis / proteasome binding / protein monoubiquitination / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / cellular response to unfolded protein / error-prone translesion synthesis / ubiquitin ligase complex / ERAD pathway / mitotic G1 DNA damage checkpoint signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA
Similarity search - Function
E3 ubiquitin-protein ligase UBR-like, C-terminal / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / : / Ubiquitin-conjugating enzyme, active site ...E3 ubiquitin-protein ligase UBR-like, C-terminal / Proteolysis_6 C-terminal / E3 ubiquitin-protein ligase UBR1-like, winged-helix domain / E3 ubiquitin-protein ligase UBR1-like / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 2 / Polyubiquitin-C / E3 ubiquitin-protein ligase UBR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Homo sapiens (human) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsPan M / Zheng Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2021
Title: Structural insights into Ubr1-mediated N-degron polyubiquitination.
Authors: Man Pan / Qingyun Zheng / Tian Wang / Lujun Liang / Junxiong Mao / Chong Zuo / Ruichao Ding / Huasong Ai / Yuan Xie / Dong Si / Yuanyuan Yu / Lei Liu / Minglei Zhao /
Abstract: The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N- ...The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway. How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1.
History
DepositionApr 8, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-7mex
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23806.png

Downloads & links

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Map

FileDownload / File: emd_23806.map.gz / Format: CCP4 / Size: 52.7 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.)
1.06 Å/pix.
x 240 pix.
= 255.12 Å		1.06 Å/pix.
x 240 pix.
= 255.12 Å		1.06 Å/pix.
x 240 pix.
= 255.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.019436516 - 0.06398185
Average (Standard dev.)0.0000051471525 (±0.002716939)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 255.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z255.120255.120255.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0190.0640.000

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Supplemental data

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Mask #1

Fileemd_23806_msk_1.map
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Additional map: #1

Fileemd_23806_additional_1.map
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Half map: #2

Fileemd_23806_half_map_1.map
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Half map: #1

Fileemd_23806_half_map_2.map
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Sample components

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Entire : yeast Ubr1 in complex with Ubc2 and N-degron

EntireName: yeast Ubr1 in complex with Ubc2 and N-degron
Components
  • Complex: yeast Ubr1 in complex with Ubc2 and N-degron
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 2
    • Protein or peptide: N-degron
    • Protein or peptide: E3 ubiquitin-protein ligase UBR1
  • Ligand: ZINC ION

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Supramolecule #1: yeast Ubr1 in complex with Ubc2 and N-degron

SupramoleculeName: yeast Ubr1 in complex with Ubc2 and N-degron / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.622922 KDa
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

UniProtKB: Polyubiquitin-C

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Macromolecule #2: Ubiquitin-conjugating enzyme E2 2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.203389 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
TPARRRLMRD FKRMKEDAPP GVSASPLPDN VMVWNAMIIG PADTPYEDGT FRLLLEFDEE YPNKPPHVKF LSEMFHPNVY ANGEICLDI LQNRWTPTYD VASILTSIQS LFNDPNPASP ANVEAATLFK DHKSQYVKRV KETVEKSWED D

UniProtKB: Ubiquitin-conjugating enzyme E2 2

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Macromolecule #3: N-degron

MacromoleculeName: N-degron / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 4.571223 KDa
SequenceString:
RHGSGSGAWL LPVSLVKRKT TLAPNTQTAS PPSYRALADS LMQ

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Macromolecule #4: E3 ubiquitin-protein ligase UBR1

MacromoleculeName: E3 ubiquitin-protein ligase UBR1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 225.10275 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSVADDDLGS LQGHIRRTLR SIHNLPYFRY TRGPTERADM SRALKEFIYR YLYFVISNSG ENLPTLFNAH PKQKLSNPEL TVFPDSLED AVDIDKITSQ QTIPFYKIDE SRIGDVHKHT GRNCGRKFKI GEPLYRCHEC GCDDTCVLCI HCFNPKDHVN H HVCTDICT ...String:
MSVADDDLGS LQGHIRRTLR SIHNLPYFRY TRGPTERADM SRALKEFIYR YLYFVISNSG ENLPTLFNAH PKQKLSNPEL TVFPDSLED AVDIDKITSQ QTIPFYKIDE SRIGDVHKHT GRNCGRKFKI GEPLYRCHEC GCDDTCVLCI HCFNPKDHVN H HVCTDICT EFTSGICDCG DEEAWNSPLH CKAEEQENDI SEDPATNADI KEEDVWNDSV NIALVELVLA EVFDYFIDVF NQ NIEPLPT IQKDITIKLR EMTQQGKMYE RAQFLNDLKY ENDYMFDGTT TAKTSPSNSP EASPSLAKID PENYTVIIYN DEY HNYSQA TTALRQGVPD NVHIDLLTSR IDGEGRAMLK CSQDLSSVLG GFFAVQTNGL SATLTSWSEY LHQETCKYII LWIT HCLNI PNSSFQTTFR NMMGKTLCSE YLNATECRDM TPVVEKYFSN KFDKNDPYRY IDLSILADGN QIPLGHHKIL PESST HSLS PLINDVETPT SRTYSNTRLQ HILYFDNRYW KRLRKDIQNV IIPTLASSNL YKPIFCQQVV EIFNHITRSV AYMDRE PQL TAIRECVVQL FTCPTNAKNI FENQSFLDIV WSIIDIFKEF CKVEGGVLIW QRVQKSNLTK SYSISFKQGL YTVETLL SK VHDPNIPLRP KEIISLLTLC KLFNGAWKIK RKEGEHVLHE DQNFISYLEY TTSIYSIIQT AEKVSEKSKD SIDSKLFL N AIRIISSFLG NRSLTYKLIY DSHEVIKFSV SHERVAFMNP LQTMLSFLIE KVSLKDAYEA LEDCSDFLKI SDFSLRSVV LCSQIDVGFW VRNGMSVLHQ ASYYKNNPEL GSYSRDIHLN QLAILWERDD IPRIIYNILD RWELLDWFTG EVDYQHTVYE DKISFIIQQ FIAFIYQILT ERQYFKTFSS LKDRRMDQIK NSIIYNLYMK PLSYSKLLRS VPDYLTEDTT EFDEALEEVS V FVEPKGLA DNGVFKLKAS LYAKVDPLKL LNLENEFESS ATIIKSHLAK DKDEIAKVVL IPQVSIKQLD KDALNLGAFT RN TVFAKVV YKLLQVCLDM EDSTFLNELL HLVHGIFRDD ELINGKDSIP EAYLSKPICN LLLSIANAKS DVFSESIVRK ADY LLEKMI MKKPNELFES LIASFGNQYV NDYKDKKLRQ GVNLQETEKE RKRRLAKKHQ ARLLAKFNNQ QTKFMKEHES EFDE QDNDV DMVGEKVYES EDFTCALCQD SSSTDFFVIP AYHDHSPIFR PGNIFNPNEF MPMWDGFYND DEKQAYIDDD VLEAL KENG SCGSRKVFVS CNHHIHHNCF KRYVQKKRFS SNAFICPLCQ TFSNCTLPLC QTSKANTGLS LDMFLESELS LDTLSR LFK PFTEENYRTI NSIFSLMISQ CQGFDKAVRK RANFSHKDVS LILSVHWANT ISMLEIASRL EKPYSISFFR SREQKYK TL KNILVCIMLF TFVIGKPSME FEPYPQQPDT VWNQNQLFQY IVRSALFSPV SLRQTVTEAL TTFSRQFLRD FLQGLSDA E QVTKLYAKAS KIGDVLKVSE QMLFALRTIS DVRMEGLDSE SIIYDLAYTF LLKSLLPTIR RCLVFIKVLH ELVKDSENE TLVINGHEVE EELEFEDTAE FVNKALKMIT EKESLVDLLT TQESIVSHPY LENIPYEYCG IIKLIDLSKY LNTYVTQSKE IKLREERSQ HMKNADNRLD FKICLTCGVK VHLRADRHEM TKHLNKNCFK PFGAFLMPNS SEVCLHLTQP PSNIFISAPY L NSHGEVGR NAMRRGDLTT LNLKRYEHLN RLWINNEIPG YISRVMGDEF RVTILSNGFL FAFNREPRPR RIPPTDEDDE DM EEGEDGF FTEGNDEMDV DDETGQAANL FGVGAEGIAG GGVRDFFQFF ENFRNTLQPQ GNGDDDAPQN PPPILQFLGP QFD GATIIR NTNPRNLDED DSDDNDDSDE REIW

UniProtKB: E3 ubiquitin-protein ligase UBR1

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 7 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: SGD implemented in RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 232915
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7mex:
Structure of yeast Ubr1 in complex with Ubc2 and N-degron

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