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Yorodumi- EMDB-23807: Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinate... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23807 | |||||||||
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Title | Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron | |||||||||
Map data | ||||||||||
Sample |
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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 / error-free postreplication DNA repair / HULC complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / 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 / error-free postreplication DNA repair / HULC complex / proteasome regulatory particle binding / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / meiotic DNA double-strand break formation / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / telomere maintenance via recombination / proteasome regulatory particle, base subcomplex / ribosome-associated ubiquitin-dependent protein catabolic process / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / fat pad development / DNA duplex unwinding / error-free translesion synthesis / sporulation resulting in formation of a cellular spore / female gonad development / proteasome binding / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / subtelomeric heterochromatin formation / error-prone translesion synthesis / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / energy homeostasis / regulation of neuron apoptotic process / : / 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 / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / mitotic G1 DNA damage checkpoint signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Homo sapiens (human) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 Å | |||||||||
Authors | Pan M / Zheng Q / Wang T / Liang L / Yu Y / Liu L / Zhao M | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23807.map.gz | 49.5 MB | EMDB map data format | |
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Header (meta data) | emd-23807-v30.xml emd-23807.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
Images | emd_23807.png | 167.9 KB | ||
Masks | emd_23807_msk_1.map | 64 MB | Mask map | |
Others | emd_23807_additional_1.map.gz emd_23807_half_map_1.map.gz emd_23807_half_map_2.map.gz | 59.8 MB 49.6 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23807 | HTTPS FTP |
-Related structure data
Related structure data | 7meyMC 7mexC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10902 (Title: Single-particle cryoEM data of yeast Ubr1-Ubc2-Ub-Ub-N-degron complex (elongation) Data size: 2.9 TB Data #1: Unaligned movie data of yeast Ubr1-Ubc2-Ub-Ub-N-degron complex (elongation complex) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23807.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23807_msk_1.map | ||||||||||||
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-Additional map: #1
File | emd_23807_additional_1.map | ||||||||||||
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-Half map: #2
File | emd_23807_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_23807_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Entire | Name: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron |
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Components |
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-Supramolecule #1: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Supramolecule | Name: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
-Macromolecule #1: E3 ubiquitin-protein ligase UBR1
Macromolecule | Name: E3 ubiquitin-protein ligase UBR1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 225.10275 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae S288C (yeast) |
Sequence | String: 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 |
-Macromolecule #2: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.493741 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRG |
-Macromolecule #3: Ubiquitin-conjugating enzyme E2 2
Macromolecule | Name: Ubiquitin-conjugating enzyme E2 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 19.725662 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSTPARRRLM RDFKRMKEDA PPGVSASPLP DNVMVWNAMI IGPADTPYED GTFRLLLEFD EEYPNKPPHV KFLSEMFHPN VYANGEICL DILQNRWTPT YDVASILTSI QSLFNDPNPA SPANVEAATL FKDHKSQYVK RVKETVEKSW EDDMDDMDDD D DDDDDDDD DEAD |
-Macromolecule #4: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.519778 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG |
-Macromolecule #5: Monoubiquitinated N-degron
Macromolecule | Name: Monoubiquitinated N-degron / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 4.571223 KDa |
Sequence | String: RHGSGSGAWL LPVSLVKRKT TLAPNTQTAS PPSYRALADS LMQ |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #7: 2-(ethylamino)ethane-1-thiol
Macromolecule | Name: 2-(ethylamino)ethane-1-thiol / type: ligand / ID: 7 / Number of copies: 1 / Formula: Z3V |
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Molecular weight | Theoretical: 105.202 Da |
Chemical component information | ChemComp-Z3V: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Startup model | Type of model: OTHER / Details: SGD method in RELION 3.1 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1) |
Final 3D classification | Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 65088 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7mey: |