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- EMDB-26615: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UB... -

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Basic information

Entry
Database: EMDB / ID: EMD-26615
TitleComplex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UBE2O-Ub)
Map dataSharpened map
Sample
  • Complex: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UBE2O-Ub)
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
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-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26615.png

Downloads & links

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Map

FileDownload / File: emd_26615.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.050071176 - 0.088384494
Average (Standard dev.)6.6220855e-05 (±0.0012920994)
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_26615_additional_1.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Additional map: Unsharpened map

Fileemd_26615_additional_2.map
AnnotationUnsharpened map
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Half map: Half map 1

Fileemd_26615_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Half map: Half map 2

Fileemd_26615_half_map_2.map
AnnotationHalf map 2
Projections & Slices
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Sample components

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Entire : Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UB...

EntireName: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UBE2O-Ub)
Components
  • Complex: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UBE2O-Ub)

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Supramolecule #1: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UB...

SupramoleculeName: Complex of UBE2O with NAP1L1 and ubiquitylated uL2 (focused on UBE2O-Ub)
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

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: 639300
FSC plot (resolution estimation)

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