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- EMDB-23807: Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinate... -

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Entry
Database: EMDB / ID: EMD-23807
TitleStructure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Map data
Sample
  • Complex: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
    • Protein or peptide: E3 ubiquitin-protein ligase UBR1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 2
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Monoubiquitinated N-degron
  • Ligand: ZINC ION
  • Ligand: 2-(ethylamino)ethane-1-thiol
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 / proteasome regulatory particle binding / error-free postreplication DNA repair / meiotic DNA double-strand break formation ...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 / proteasome regulatory particle binding / error-free postreplication DNA repair / meiotic DNA double-strand break formation / ubiquitin-dependent protein catabolic process via the N-end rule pathway / stress-induced homeostatically regulated protein degradation pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / ribosome-associated ubiquitin-dependent protein catabolic process / error-free translesion synthesis / E2 ubiquitin-conjugating enzyme / sporulation resulting in formation of a cellular spore / symbiont entry into host cell via disruption of host cell envelope / virus tail / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein monoubiquitination / cellular response to unfolded protein / ubiquitin ligase complex / error-prone translesion synthesis / subtelomeric heterochromatin formation / ERAD pathway / mitotic G1 DNA damage checkpoint signaling / double-strand break repair via homologous recombination / DNA-templated transcription termination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / DNA repair / chromatin / zinc ion binding / ATP binding / nucleus / cytoplasm
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 / : ...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 / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 2 / Tail fiber / 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: 3.67 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

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

emd_23807.png

Downloads & links

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Map

FileDownload / File: emd_23807.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.128 Å		1.06 Å/pix.
x 256 pix.
= 272.128 Å		1.06 Å/pix.
x 256 pix.
= 272.128 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-0.02186463 - 0.061399642
Average (Standard dev.)0.00010982538 (±0.0025003692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.128 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.128272.128272.128
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0220.0610.000

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Supplemental data

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Mask #1

Fileemd_23807_msk_1.map
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Additional map: #1

Fileemd_23807_additional_1.map
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Half map: #2

Fileemd_23807_half_map_1.map
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Half map: #1

Fileemd_23807_half_map_2.map
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Sample components

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

EntireName: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Components
  • Complex: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
    • Protein or peptide: E3 ubiquitin-protein ligase UBR1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 2
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Monoubiquitinated N-degron
  • Ligand: ZINC ION
  • Ligand: 2-(ethylamino)ethane-1-thiol

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

SupramoleculeName: yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: E3 ubiquitin-protein ligase UBR1

MacromoleculeName: E3 ubiquitin-protein ligase UBR1 / type: protein_or_peptide / ID: 1 / 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 #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.493741 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRG

UniProtKB: Tail fiber

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Macromolecule #3: Ubiquitin-conjugating enzyme E2 2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 2 / type: protein_or_peptide / ID: 3 / 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: 19.725662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTPARRRLM RDFKRMKEDA PPGVSASPLP DNVMVWNAMI IGPADTPYED GTFRLLLEFD EEYPNKPPHV KFLSEMFHPN VYANGEICL DILQNRWTPT YDVASILTSI QSLFNDPNPA SPANVEAATL FKDHKSQYVK RVKETVEKSW EDDMDDMDDD D DDDDDDDD DEAD

UniProtKB: Ubiquitin-conjugating enzyme E2 2

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Macromolecule #4: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.519778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG

UniProtKB: Tail fiber

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Macromolecule #5: Monoubiquitinated N-degron

MacromoleculeName: Monoubiquitinated N-degron / type: protein_or_peptide / ID: 5 / 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 #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: 2-(ethylamino)ethane-1-thiol

MacromoleculeName: 2-(ethylamino)ethane-1-thiol / type: ligand / ID: 7 / Number of copies: 1 / Formula: Z3V
Molecular weightTheoretical: 105.202 Da
Chemical component information

ChemComp-Z3V:
2-(ethylamino)ethane-1-thiol

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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 method in RELION 3.1
Final reconstructionApplied 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
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)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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