Nature - USA (2020-02-13)

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nature research | reporting summary

October 2018

Data

Policy information about availability of data

All manuscripts must include a data availability statement. This statement should provide the following information, where applicable:

• Accession codes, unique identifiers, or web links for publicly available datasets


• A list of figures that have associated raw data


• A description of any restrictions on data availability
  The authors declare that the data supporting the findings of this study are available within the paper. Supplementary data (Supplementary Video1, 2, 3, 4, 5, 6, 7;
  and Supplementary Figure 1) and Source data for all quantification (Fig. 1c, 1d, 2c, 3a, 3b, 3c, 4a, 4b, 4d; Extended Data Fig. 1e, 3a, 3b, 3c, 5a, 5c, 6c, 7a, 8d, 8e, 9d)
  are provided with the online version of the paper. Supplementary Figure 1 contains uncropped images of blots and gels. Raw images of Cryo-ET have been
  deposited to the Electrone Microscopy Data Bank under accession code EMD-10494. The mass spectrometry proteomics data have been deposited to the
  ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD01637 and PXD016369. All other datasets analysed in the current
  study are available from the corresponding author upon reasonable requests.

Field-specific reporting

Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences

For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design

All studies must disclose on these points even when the disclosure is negative.

Sample size We did not compute statistical analyses to predetermine sample sizes. Sample sizes were chosen based on similar published studies

elsewhere. All analyzes were at least two and more independent samples (for n, see figure legends), and in each experimental repeat yielding

highly similar results.

Data exclusions No data exclusions.

Replication We have reproduced all our results in a minimum of two independent experimental repeats. Experimental findings have been either^

reproduced independently by co-authors of the paper using the same experimental conditions.

Randomization Randomization was not required as no human participants or animal models were reported in this manuscript and experiments were

performed on specified cell lines.

Blinding Many microscopy images were blinded and analyzed in an automated fashion.

Reporting for specific materials, systems and methods

We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material,

system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

n/a Involved in the study

Antibodies

Eukaryotic cell lines

Palaeontology

Animals and other organisms

Human research participants

Clinical data

Methods

n/a Involved in the study

ChIP-seq

Flow cytometry

MRI-based neuroimaging

Antibodies

Antibodies used Antibody (clone), dilution, Supplier, Cat. number, Lot number:

Ubiquitin, 1:500 (for IF) or 1:1000 (for WB), Dako, Z0458, 00082271

Ubiquitin (FK2), 1: 500, Nippon Bio-Test Laboratories, NBT-MFK003, C7070

Ubiquitin Lys48-Specific (Apu2), 1:500 (for IF) or 1:1000 (for WB), Millipore, 05-1307, 2918991

Ubiquitin Lys63-Specific (Apu3), 1:500, Millipore, 05-1308, 3137755

PSMB2, 1:1000, Enzo, BML-PW8890, Z03617b