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- EMDB-26614: Complex of UBE2O with NAP1L1 -

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Basic information

Entry
Database: EMDB / ID: EMD-26614
TitleComplex of UBE2O with NAP1L1
Map dataSharpened map
Sample
  • Complex: Complex of UBE2O with NAP1L1
    • Protein or peptide: (E3-independent) E2 ubiquitin-conjugating enzyme
    • Protein or peptide: Nucleosome assembly protein 1-like 1
KeywordsUbiquitylation / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


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 K63-linked ubiquitination / protein monoubiquitination / ubiquitin-protein transferase activity ...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 K63-linked ubiquitination / protein monoubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / melanosome / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / nucleosome assembly / histone binding / DNA replication / nuclear body / positive regulation of cell population proliferation / chromatin binding / chromatin / RNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
UBE2O, ubiquitin binding SH3-C domain / UBE2O, tandem tSH3-B domain / UBE2O, N-terminal SH3-A domain / UBE2O, SH3-B domain / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...UBE2O, ubiquitin binding SH3-C domain / UBE2O, tandem tSH3-B domain / UBE2O, N-terminal SH3-A domain / UBE2O, SH3-B domain / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / 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
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1 / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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
Other privateVallee 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 9, 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_26614.png

Downloads & links

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Map

FileDownload / File: emd_26614.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 280.5 Å		0.83 Å/pix.
x 340 pix.
= 280.5 Å		0.83 Å/pix.
x 340 pix.
= 280.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-4.5323787 - 5.7783556
Average (Standard dev.)-0.0015465204 (±0.06794154)
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: Unsharpened map

Fileemd_26614_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: deepEMhancer sharpened map

Fileemd_26614_additional_2.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half map 1

Fileemd_26614_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_26614_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

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

EntireName: Complex of UBE2O with NAP1L1
Components
  • Complex: Complex of UBE2O with NAP1L1
    • Protein or peptide: (E3-independent) E2 ubiquitin-conjugating enzyme
    • Protein or peptide: Nucleosome assembly protein 1-like 1

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Supramolecule #1: Complex of UBE2O with NAP1L1

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

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Macromolecule #1: (E3-independent) E2 ubiquitin-conjugating enzyme

MacromoleculeName: (E3-independent) E2 ubiquitin-conjugating enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: (E3-independent) E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 147.187188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGAWSHPQFE KGSWSHPQFE KGPAGSENLY FQGSGIRDRT MADPAAPTPA APAPAQAPAP APEAVPAPAA APVPAPAPA SDSASGPSSD SGPEAGSQRL LFSHDLVSGR YRGSVHFGLV RLIHGEDSDS EGEEEGRGSS GCSEAGGAGH E EGRASPLR ...String:
MASWSHPQFE KGAWSHPQFE KGSWSHPQFE KGPAGSENLY FQGSGIRDRT MADPAAPTPA APAPAQAPAP APEAVPAPAA APVPAPAPA SDSASGPSSD SGPEAGSQRL LFSHDLVSGR YRGSVHFGLV RLIHGEDSDS EGEEEGRGSS GCSEAGGAGH E EGRASPLR RGYVRVQWYP EGVKQHVKET KLKLEDRSVV PRDVVRHMRS TDSQCGTVID VNIDCAVKLI GTNCIIYPVN SK DLQHIWP FMYGDYIAYD CWLGKVYDLK NQIILKLSNG ARCSMNTEDG AKLYDVCPHV SDSGLFFDDS YGFYPGQVLI GPA KIFSSV QWLSGVKPVL STKSKFRVVV EEVQVVELKV TWITKSFCPG GTDSVSPPPS VITQENLGRV KRLGCFDHAQ RQLG ERCLY VFPAKVEPAK IAWECPEKNC AQGEGSMAKK VKRLLKKQVV RIMSCSPDTQ CSRDHSMEDP DKKGESKTKS EAESA SPEE TPDGSASPVE MQDEGAEEPH EAGEQLPPFL LKEGRDDRLH SAEQDADDEA ADDTDDTSSV TSSASSTTSS QSGSGT SRK KSIPLSIKNL KRKHKRKKNK ITRDFKPGDR VAVEVVTTMT SADVMWQDGS VECNIRSNDL FPVHHLDNNE FCPGDFV VD KRVQSCPDPA VYGVVQSGDH IGRTCMVKWF KLRPSGDDVE LIGEEEDVSV YDIADHPDFR FRTTDIVIRI GNTEDGAP H KEDEPSVGQV ARVDVSSKVE VVWADNSKTI ILPQHLYNIE SEIEESDYDS VEGSTSGASS DEWEDDSDSW ETDNGLVED EHPKIEEPPI PPLEQPVAPE DKGVVISEEA ATAAVQGAVA MAAPMAGLME KAGKDGPPKS FRELKEAIKI LESLKNMTVE QLLTGSPTS PTVEPEKPTR EKKFLDDIKK LQENLKKTLD NVAIVEEEKM EAVPDVERKE DKPEGQSPVK AEWPSETPVL C QQCGGKPG VTFTSAKGEV FSVLEFAPSN HSFKKIEFQP PEAKKFFSTV RKEMALLATS LPEGIMVKTF EDRMDLFSAL IK GPTRTPY EDGLYLFDIQ LPNIYPAVPP HFCYLSQCSG RLNPNLYDNG KVKVSLLGTW IGKGTERWTS KSSLLQVLIS IQG LILVNE PYYNEAGFDS DRGLQEGYEN SRCYNEMALI RVVQSMTQLV RRPPEVFEQE IRQHFSTGGW RLVNRIESWL ETHA LLEKA QALPNGVPKA SSSPEPPAVA ELSDSGQQEP EDGGPAPGEA SQGSDSEGGA QGLASASRDH TDQTSETAPD ASVPP SVKP KKRRKSYRSF LPEKSGYPDI GFPLFPLSKG FIKSIRGVLT QFRAALLEAG MPECTEDK

UniProtKB: (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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 447881
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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