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- EMDB-26612: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 -

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Basic information

Entry
Database: EMDB / ID: EMD-26612
TitleComplex of UBE2O with NAP1L1 and ubiquitylated uL2
Map dataSharpened map
Sample
  • Complex: Complex of UBE2O with NAP1L1 and ubiquitylated uL2
    • Protein or peptide: Nucleosome assembly protein 1-like 1
  • Protein or peptide: Ubiquitin,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion
KeywordsUbiquitylation / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


histone chaperone activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of neural precursor cell proliferation / positive regulation of BMP signaling pathway / retrograde transport, endosome to Golgi / positive regulation of neurogenesis / Protein hydroxylation / ubiquitin conjugating enzyme activity / protein monoubiquitination / Peptide chain elongation ...histone chaperone activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of neural precursor cell proliferation / positive regulation of BMP signaling pathway / retrograde transport, endosome to Golgi / positive regulation of neurogenesis / Protein hydroxylation / ubiquitin conjugating enzyme activity / protein monoubiquitination / Peptide chain elongation / protein K63-linked ubiquitination / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / 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 / cytosolic ribosome / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / 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 / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Ribosomal protein L2, archaeal-type / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family ...Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Ribosomal protein L2, archaeal-type / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ubiquitin homologues / Ribosomal protein L2, domain 3 / Ubiquitin-like domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ubiquitin domain profile. / Ribosomal Proteins L2, RNA binding domain / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Ubiquitin-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1 / Large ribosomal subunit protein uL2 / Ubiquitin-ribosomal protein eL40 fusion protein / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYip MCJ / Sedor SF / Shao S
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137415 United States
David and Lucile Packard Foundation2019-69660 United States
The Vallee Foundation
American Heart Association287375208 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F31HL157976 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Mechanism of client selection by the protein quality-control factor UBE2O.
Authors: Matthew C J Yip / Samantha F Sedor / Sichen Shao /
Abstract: The E2/E3 enzyme UBE2O ubiquitylates diverse clients to mediate important processes, including targeting unassembled 'orphan' proteins for quality control and clearing ribosomes during erythropoiesis. ...The E2/E3 enzyme UBE2O ubiquitylates diverse clients to mediate important processes, including targeting unassembled 'orphan' proteins for quality control and clearing ribosomes during erythropoiesis. How quality-control factors, such as UBE2O, select clients on the basis of heterogeneous features is largely unknown. Here, we show that UBE2O client selection is regulated by ubiquitin binding and a cofactor, NAP1L1. Attaching a single ubiquitin onto a client enhances UBE2O binding and multi-mono-ubiquitylation. UBE2O also repurposes the histone chaperone NAP1L1 as an adapter to recruit a subset of clients. Cryo-EM structures of human UBE2O in complex with NAP1L1 reveal a malleable client recruitment interface that is autoinhibited by the intrinsically reactive UBC domain. Adding a ubiquitylated client identifies a distinct ubiquitin-binding SH3-like domain required for client selection. Our findings reveal how multivalency and a feed-forward mechanism drive the selection of protein quality-control clients.
History
DepositionApr 8, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26612.png

Downloads & links

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Map

FileDownload / File: emd_26612.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.153266 - 2.953773
Average (Standard dev.)-0.0016925418 (±0.04302167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 280.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer sharpened map

Fileemd_26612_additional_1.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_26612_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_26612_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_26612_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of UBE2O with NAP1L1 and ubiquitylated uL2

EntireName: Complex of UBE2O with NAP1L1 and ubiquitylated uL2
Components
  • Complex: Complex of UBE2O with NAP1L1 and ubiquitylated uL2
    • Protein or peptide: Nucleosome assembly protein 1-like 1
  • Protein or peptide: Ubiquitin,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion

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Supramolecule #1: Complex of UBE2O with NAP1L1 and ubiquitylated uL2

SupramoleculeName: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-...

MacromoleculeName: Ubiquitin,60S ribosomal protein L8,(E3-independent) E2 ubiquitin-conjugating enzyme fusion
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: (E3-independent) E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 190.728406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGAWSHPQFE KGSWSHPQFE KGPAGSENLY FQGSGIRMQI FVKTLTGKTI TLEVEPSDTI ENVKAKIQDK EGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR LRGVGSMGRV IRGQRKGAGS VFRAHVKHRK GAARLRAVDF A ERHGYIKG ...String:
MASWSHPQFE KGAWSHPQFE KGSWSHPQFE KGPAGSENLY FQGSGIRMQI FVKTLTGKTI TLEVEPSDTI ENVKAKIQDK EGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR LRGVGSMGRV IRGQRKGAGS VFRAHVKHRK GAARLRAVDF A ERHGYIKG IVKDIIHDPG RGAPLAKVVF RDPYRFKKRT ELFIAAEGIH TGQFVYCGKK AQLNVGNVLP VGTMPEGTIV CC LEEKPGD RGKLARASGN YATVISHNPE TKKTRVKLPS GSKKVISSAN RAVVGVVAGG GRIDKPILKA GRAYHKYKAK RNC WPRVRG VAMNPVEHPF GGGNHQHIGK PSTIRRDAPA GRKVGLIAAR RTGRLRGTKT VQEKENGGSG LEVLFQGPGG SGGG SGLEV LFQGPGGSGY PYDVPDYAGY PYDVPDYAGS YPYDVPDYAG SAIRDRTMAD PAAPTPAAPA PAQAPAPAPE AVPAP AAAP VPAPAPASDS ASGPSSDSGP EAGSQRLLFS HDLVSGRYRG SVHFGLVRLI HGEDSDSEGE EEGRGSSGCS EAGGAG HEE GRASPLRRGY VRVQWYPEGV KQHVKETKLK LEDRSVVPRD VVRHMRSTDS QCGTVIDVNI DCAVKLIGTN CIIYPVN SK DLQHIWPFMY GDYIAYDCWL GKVYDLKNQI ILKLSNGARC SMNTEDGAKL YDVCPHVSDS GLFFDDSYGF YPGQVLIG P AKIFSSVQWL SGVKPVLSTK SKFRVVVEEV QVVELKVTWI TKSFCPGGTD SVSPPPSVIT QENLGRVKRL GCFDHAQRQ LGERCLYVFP AKVEPAKIAW ECPEKNCAQG EGSMAKKVKR LLKKQVVRIM SCSPDTQCSR DHSMEDPDKK GESKTKSEAE SASPEETPD GSASPVEMQD EGAEEPHEAG EQLPPFLLKE GRDDRLHSAE QDADDEAADD TDDTSSVTSS ASSTTSSQSG S GTSRKKSI PLSIKNLKRK HKRKKNKITR DFKPGDRVAV EVVTTMTSAD VMWQDGSVEC NIRSNDLFPV HHLDNNEFCP GD FVVDKRV QSCPDPAVYG VVQSGDHIGR TCMVKWFKLR PSGDDVELIG EEEDVSVYDI ADHPDFRFRT TDIVIRIGNT EDG APHKED EPSVGQVARV DVSSKVEVVW ADNSKTIILP QHLYNIESEI EESDYDSVEG STSGASSDEW EDDSDSWETD NGLV EDEHP KIEEPPIPPL EQPVAPEDKG VVISEEAATA AVQGAVAMAA PMAGLMEKAG KDGPPKSFRE LKEAIKILES LKNMT VEQL LTGSPTSPTV EPEKPTREKK FLDDIKKLQE NLKKTLDNVA IVEEEKMEAV PDVERKEDKP EGQSPVKAEW PSETPV LCQ QCGGKPGVTF TSAKGEVFSV LEFAPSNHSF KKIEFQPPEA KKFFSTVRKE MALLATSLPE GIMVKTFEDR MDLFSAL IK GPTRTPYEDG LYLFDIQLPN IYPAVPPHFC YLSQCSGRLN PNLYDNGKVK VSLLGTWIGK GTERWTSKSS LLQVLISI Q GLILVNEPYY NEAGFDSDRG LQEGYENSRC YNEMALIRVV QSMTQLVRRP PEVFEQEIRQ HFSTGGWRLV NRIESWLET HALLEKAQAL PNGVPKASSS PEPPAVAELS DSGQQEPEDG GPAPGEASQG SDSEGGAQGL ASASRDHTDQ TSETAPDASV PPSVKPKKR RKSYRSFLPE KSGYPDIGFP LFPLSKGFIK SIRGVLTQFR AALLEAGMPE CTEDK

UniProtKB: Ubiquitin-ribosomal protein eL40 fusion protein, Large ribosomal subunit protein uL2, (E3-independent) E2 ubiquitin-conjugating enzyme

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Macromolecule #2: Nucleosome assembly protein 1-like 1

MacromoleculeName: Nucleosome assembly protein 1-like 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.363898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKAGSADID NKEQSELDQD LDDVEEVEEE ETGEETKLKA RQLTVQMMQN PQILAALQER LDGLVETPT GYIESLPRVV KRRVNALKNL QVKCAQIEAK FYEEVHDLER KYAVLYQPLF DKRFEIINAI YEPTEEECEW K PDEEDEIS ...String:
MDYKDHDGDY KDHDIDYKDD DDKAGSADID NKEQSELDQD LDDVEEVEEE ETGEETKLKA RQLTVQMMQN PQILAALQER LDGLVETPT GYIESLPRVV KRRVNALKNL QVKCAQIEAK FYEEVHDLER KYAVLYQPLF DKRFEIINAI YEPTEEECEW K PDEEDEIS EELKEKAKIE DEKKDEEKED PKGIPEFWLT VFKNVDLLSD MVQEHDEPIL KHLKDIKVKF SDAGQPMSFV LE FHFEPNE YFTNEVLTKT YRMRSEPDDS DPFSFDGPEI MGCTGCQIDW KKGKNVTLKT IKKKQKHKGR GTVRTVTKTV SND SFFNFF APPEVPESGD LDDDAEAILA ADFEIGHFLR ERIIPRSVLY FTGEAIEDDD DDYDEEGEEA DEEGEEEGDE ENDP DYDPK KDQNPAECKQ Q

UniProtKB: Nucleosome assembly protein 1-like 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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201743
FSC plot (resolution estimation)

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