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

Basic information

Entry

Database: EMDB / ID: EMD-26612

• Title: Complex of UBE2O with NAP1L1 and ubiquitylated uL2
• Map data: Sharpened 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

• Keywords: Ubiquitylation / CYTOSOLIC PROTEIN

Function / homology

Function:

histone chaperone activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / positive regulation of neural precursor cell proliferation / retrograde transport, endosome to Golgi / positive regulation of neurogenesis / ubiquitin conjugating enzyme activity / Protein hydroxylation / Peptide chain elongation / 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 / protein K63-linked ubiquitination / Viral mRNA Translation / protein monoubiquitination / 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 / cytosolic ribosome / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex

Domain/homology:

UBE2O, SH3-B domain / UBE2O, ubiquitin binding SH3-C domain / UBE2O, tandem tSH3-B domain / UBE2O, N-terminal SH3-A domain / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Ribosomal protein L2, archaeal-type / 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein L2 signature. / Ubiquitin family / Ribosomal protein L2, conserved site / Ribosomal protein L2, domain 3 / Ubiquitin homologues / Ubiquitin domain profile. / 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 Proteins L2, RNA binding domain / Ribosomal protein L2 / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Ubiquitin-like domain superfamily / Nucleic acid-binding, OB-fold

Component:

Nucleosome assembly protein 1-like 1 / Large ribosomal subunit protein uL2 / Ubiquitin-ribosomal protein eL40 fusion protein / (E3-independent) E2 ubiquitin-conjugating enzyme

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: Yip MCJ / Sedor SF / Shao S

Funding support

United States, 5 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	DP2GM137415	United States
David and Lucile Packard Foundation	2019-69660	United States
The Vallee Foundation
American Heart Association	287375208	United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	F31HL157976	United States

• Citation: Journal: 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. 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

Deposition	Apr 8, 2022	-
Header (metadata) release	Aug 3, 2022	-
Map release	Aug 3, 2022	-
Update	Feb 14, 2024	-
Current status	Feb 14, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_26612.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Sharpened map
• Voxel size: X=Y=Z: 0.825 Å

Density

Contour Level	By AUTHOR: 0.3
Minimum - Maximum	-2.153266 - 2.953773
Average (Standard dev.)	-0.0016925418 (±0.04302167)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 340 340 340 Spacing 340 340 340
Cell	A=B=C: 280.5 Å α=β=γ: 90.0 °

Supplemental data

Additional map: deepEMhancer sharpened map

• File: emd_26612_additional_1.map
• Annotation: deepEMhancer sharpened map

Additional map: Unsharpened map

• File: emd_26612_additional_2.map
• Annotation: Unsharpened map

Half map: Half map 2

• File: emd_26612_half_map_1.map
• Annotation: Half map 2

Half map: Half map 1

• File: emd_26612_half_map_2.map
• Annotation: Half map 1

Sample components

Entire : Complex of UBE2O with NAP1L1 and ubiquitylated uL2

• Entire: Name: 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

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

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

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

• Macromolecule: Name: 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 weight: Theoretical: 190.728406 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

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

Macromolecule #2: Nucleosome assembly protein 1-like 1

• Macromolecule: Name: 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 weight: Theoretical: 48.363898 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

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

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 1 mg/mL
• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.6 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.4000000000000001 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201743
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD