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. 2016 Nov 22;9:1130–1137. doi: 10.1016/j.dib.2016.11.048

Data on the identity of non-canonical complexes formed from proteasome subunits in vivo

Lindsay J Hammack 1, Andrew R Kusmierczyk 1,
PMCID: PMC5128733  PMID: 27924301

Abstract

The dataset presented here represents analysis supplied by the local proteomics core facility on samples submitted to it in support of the article “Assembly of proteasome subunits into non-canonical complexes in vivo” Hammack and Kusmierczyk (2016) [1]. This article provides the detailed protein contents of gel slices, cut from non-denaturing polyacrylamide gels, containing distinct protein complexes visualized following gel staining. The identification of the protein contents of these complexes was carried out by liquid chromatography tandem mass-spectrometry (LC–MS/MS).

Keywords: Proteasome, Yeast, Protein complex, Mass-spectrometry, Proteomics


Specifications Table

Subject area Biology
More specific subject area Molecular biology
Type of data Excel files, word document
How data was acquired The local proteomics core facility provides fee-for-service protein identification analysis by liquid chromatography tandem mass-spectrometry.
Data format Processed
Experimental factors Purified protein complexes isolated from various yeast strains were separated by native PAGE and stained to identify individual bands.
Experimental features Gel slices, representing individual bands identified on non-denaturing polyacrylamide gels, were cut out and submitted for protein identification.
Data source location Department of Biology; Indiana University-Purdue University Indianapolis; Indianapolis, IN, USA
Data accessibility The processed data in Excel format, as supplied by the core facility, is with this article. The mass-spectrometry raw data collected by the proteomics core facility remains with the facility and was not provided to the researcher as part of the fee-for-service analysis.

Value of the data

  • The data support the identification of novel protein complexes comprised of proteasome subunits.

  • Novel protein complexes identified invite additional experiments to further characterize them.

  • Data also identify proteins associated with these novel protein complexes.

1. Data

The data contained here (Tables 1–8) are from the Excel files provided to the authors by the local proteomics core facility as part of the fee-for-service analysis of samples submitted (see Appendix). Each Excel file corresponds to a band cut out of a non-denaturing polyacrylamide gel in the referenced article [1]. Each Excel file includes information to direct the reader to the appropriate band that was analyzed. The Excel files contain details of the proteins identified in each sample submitted to the core facility, including: the number and sequence of each identified peptide, any modifications of each peptide, spectral counts, and coverage, etc. The title of each Excel file is meant to direct the reader to the actual band that was analyzed in the referenced article [1]. Additional Excel files are found in Appendix.

2. Experimental design, materials and methods

Non-denaturing polyacrylamide gel electrophoresis was carried out as described [1]. Bands (gel slices) were excised and submitted for analysis to the Indiana University School of Medicine Proteomics Core Facility. The facility carried out protein identification and provided processed data as Excel files. The Excel files were accompanied by a copy of a Word document that outlined the experimental procedure carried out by the core facility, and the subsequent data analysis, to identify the proteins within the sample. A copy of this word document is included in the Appendix.

Table 1.

Protein content of Band 1.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 236.09 78.74 3 16 90
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 228.60 79.37 1 16 114
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 201.77 88.07 22 22 78
323337524 Pre9p [Saccharomyces cerevisiae Vin13] 197.22 73.64 19 19 58
93279386 Chain S, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 183.95 83.69 19 19 60
256274381 Pba1p [Saccharomyces cerevisiae JAY291] 153.63 61.96 12 12 54
93279382 Chain O, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 152.91 52.00 12 12 65
178847521 Chain T, Yeast 20s Proteasome:glidobactin A-Complex 142.44 60.98 16 16 49
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 135.74 46.60 8 8 38
444302412 Chain R, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 109.18 59.62 17 17 34
403071955 Chain 2, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome 103.01 31.80 9 9 69
151941458 conserved protein [Saccharomyces cerevisiae YJM789] 72.71 31.84 9 9 27
151944720 22.6 kDa proteasome subunit [Saccharomyces cerevisiae YJM789] 53.84 47.47 10 10 20
93279393 Chain Z, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 31.84 35.14 5 5 12
323305986 Ump1p [Saccharomyces cerevisiae FostersB] 31.83 22.97 3 3 22
207340308 YPR103Wp-like protein [Saccharomyces cerevisiae AWRI1631] 29.60 33.10 8 8 9
323337162 Pfk26p [Saccharomyces cerevisiae Vin13] 28.55 13.68 9 9 9
207345674 YFL007Wp-like protein [Saccharomyces cerevisiae AWRI1631] 26.43 4.62 6 6 8
741845 peptidyl-Glu protease 23.26 34.72 6 6 7
259146995 Ecm29p [Saccharomyces cerevisiae EC1118] 15.98 4.13 5 5 5
736313 unknown [Saccharomyces cerevisiae] 14.84 10.44 5 5 5
226279 mitochondrial assembly factor 11.90 7.17 3 3 4
323304344 Tdh2p [Saccharomyces cerevisiae FostersB] 11.63 20.98 3 3 4

This table pertains to Band 1 from Fig. 2 in the referenced manuscript.

Table 2.

Protein content of Band 2.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 206.36 77.56 2 13 113
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 182.00 78.17 1 13 82
323337524 Pre9p [Saccharomyces cerevisiae Vin13] 144.66 77.27 18 18 43
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 141.43 83.13 19 19 57
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 96.26 46.60 8 8 27
151946074 proteasome component Y7 [Saccharomyces cerevisiae YJM789] 94.51 37.20 11 11 40
403071955 Chain 2, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome 67.94 31.03 7 7 41
172136 6-phosphofructo-2-kinase [Saccharomyces cerevisiae] 43.50 18.62 12 12 13
151944720 22.6 kDa proteasome subunit [Saccharomyces cerevisiae YJM789] 40.65 46.46 7 7 15
349577910 K7_Blm10p [Saccharomyces cerevisiae Kyokai no. 7] 39.81 6.35 11 11 13
259148570 Erg6p [Saccharomyces cerevisiae EC1118] 28.84 23.76 6 6 8
256270485 Pdc1p [Saccharomyces cerevisiae JAY291] 27.82 20.89 6 6 11
171457 enolase [Saccharomyces cerevisiae] 26.17 20.82 6 6 7
323336942 Ssc1p [Saccharomyces cerevisiae Vin13] 24.65 12.64 6 6 8
741845 peptidyl-Glu protease 24.17 36.27 6 6 8
259149737 Rpn8p [Saccharomyces cerevisiae EC1118] 24.00 16.57 4 4 7
323303909 Acs2p [Saccharomyces cerevisiae FostersB] 21.18 9.15 4 4 8
312258 PUP2 [Saccharomyces cerevisiae] 18.90 29.23 6 6 6
323355426 Rpn3p [Saccharomyces cerevisiae VL3] 18.64 15.48 5 5 6
223142 dehydrogenase isozyme I,alcohol 15.41 15.77 4 4 5
323352105 Eft2p [Saccharomyces cerevisiae VL3] 15.16 7.87 4 4 5
1103917 D-arabinono-1,4-lactone oxidase [Saccharomyces cerevisiae] 14.25 11.41 5 5 5
323333957 Rpn9p [Saccharomyces cerevisiae AWRI796] 13.22 13.80 3 3 4
323305986 Ump1p [Saccharomyces cerevisiae FostersB] 12.80 15.54 2 2 8

This table pertains to Band 2 from Fig. 2 in the referenced manuscript.

Table 3.

Protein content of Band 3.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs

444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 625.80 67.72 2 16 313
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 575.74 68.25 3 16 277
298508455 Chain U, Proteasome Activator Complex 487.69 67.40 2 14 174
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 188.85 89.71 22 22 75
93279386 Chain S, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 119.42 78.11 14 14 37
323337524 Pre9p [Saccharomyces cerevisiae Vin13] 119.35 77.27 18 18 34
93279382 Chain O, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 117.98 52.00 11 11 48
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 92.81 41.88 9 9 29
390980863 Chain T, Structure Of Yeast 20s Open-Gate Proteasome With Compound 34 90.73 51.65 9 9 27
403071955 Chain 2, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome 72.80 46.74 7 7 47
256274381 Pba1p [Saccharomyces cerevisiae JAY291] 70.73 57.25 11 11 19
312258 PUP2 [Saccharomyces cerevisiae] 58.77 44.23 13 13 15
151944720 22.6 kDa proteasome subunit [Saccharomyces cerevisiae YJM789] 45.95 47.47 8 8 14
323305986 Ump1p [Saccharomyces cerevisiae FostersB] 35.64 41.89 5 5 20
323337162 Pfk26p [Saccharomyces cerevisiae Vin13] 35.29 16.54 10 10 10
93279395 Chain 2, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 34.81 65.31 8 8 12
93279393 Chain Z, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 32.74 35.59 6 6 11
151941458 conserved protein [Saccharomyces cerevisiae YJM789] 31.70 31.46 7 7 10
207340308 YPR103Wp-like protein [Saccharomyces cerevisiae AWRI1631] 30.22 25.09 6 6 10
93279394 Chain 1, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 23.31 27.04 3 3 7
226279 mitochondrial assembly factor 19.36 15.03 6 6 6
190407817 conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a] 15.53 35.81 3 3 5
166007292 Chain E, Crystal Structure Of A Novel Chaperone Complex For Yeast 20s Proteasome Assembly 13.50 36.24 3 3 4
207345674 YFL007Wp-like protein [Saccharomyces cerevisiae AWRI1631] 12.97 2.78 4 4 4

This table pertains to Band 3 from Fig. 2 in the referenced manuscript.

Table 4.

Protein content of Band 4.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 592.98 66.14 2 17 354
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 538.85 66.67 2 17 281
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 504.52 92.59 30 30 198
298508455 Chain U, Proteasome Activator Complex 417.71 65.64 2 15 145
323348418 Pre9p [Saccharomyces cerevisiae Lalvin QA23] 268.96 91.09 22 22 84
178847521 Chain T, Yeast 20s Proteasome:glidobactin A-Complex 214.58 62.72 14 14 72
93279382 Chain O, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 197.26 52.00 12 12 70
403071955 Chain 2, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome 184.91 58.62 13 13 85
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 176.76 42.93 8 8 49
93279386 Chain S, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 166.90 82.83 17 17 57
151944720 22.6 kDa proteasome subunit [Saccharomyces cerevisiae YJM789] 115.04 43.94 9 9 48
256274381 Pba1p [Saccharomyces cerevisiae JAY291] 92.42 57.25 11 11 28
312258 PUP2 [Saccharomyces cerevisiae] 86.96 61.54 17 17 25
323305986 Ump1p [Saccharomyces cerevisiae FostersB] 70.97 45.95 5 5 51
349577910 K7_Blm10p [Saccharomyces cerevisiae Kyokai no. 7] 53.82 7.89 13 13 17
166007287 Chain B, Crystal Structure Of A Novel Chaperone Complex For Yeast 20s Proteasome Assembly 51.61 76.54 9 9 12
123624 RecName: Full=Heat shock protein SSA2 45.22 27.70 3 11 13
323306163 Ssa1p [Saccharomyces cerevisiae FostersB] 41.81 24.18 1 10 12
151941458 conserved protein [Saccharomyces cerevisiae YJM789] 38.90 28.09 6 6 13
171541 glyceraldehyde-3-phosphate dehydrogenase (G3PD) [Saccharomyces cerevisiae] 35.39 33.73 6 6 11
323337162 Pfk26p [Saccharomyces cerevisiae Vin13] 35.23 16.54 10 10 10
190407817 conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a] 29.15 37.16 5 5 10
190408474 conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a] 25.09 5.06 6 6 8
323334738 Pre7p [Saccharomyces cerevisiae AWRI796] 24.16 18.48 2 2 6
3114294 Chain Z, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution 16.06 25.00 5 5 5
121575 RecName: Full=78 kDa glucose-regulated protein homolog; Short=GRP-78; AltName: Full=Immunoglobulin heavy chain-binding protein homolog; Short=BiP; Flags: Precursor 13.13 7.62 3 4 4

This table pertains to Band 4 from Fig. 2 in the referenced manuscript.

Table 5.

Protein content of Band 5.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 1411.77 69.69 2 19 724
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 1244.29 70.24 3 19 546
298508455 Chain U, Proteasome Activator Complex 1056.66 69.60 2 17 344
323352352 Pre6p [Saccharomyces cerevisiae VL3] 771.05 65.24 1 16 235
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 114.49 79.01 17 17 47
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 82.42 51.83 10 10 24
151944720 22.6 kDa proteasome subunit [Saccharomyces cerevisiae YJM789] 80.43 47.47 10 10 27
123624 RecName: Full=Heat shock protein SSA2 79.71 34.59 5 16 26
323306163 Ssa1p [Saccharomyces cerevisiae FostersB] 78.44 30.93 2 14 24
984187 transcription factor [Saccharomyces cerevisiae] 65.14 32.41 12 12 27
312258 PUP2 [Saccharomyces cerevisiae] 62.46 58.08 14 14 20
93279393 Chain Z, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 43.29 31.08 5 5 14
93279386 Chain S, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 41.02 60.94 10 10 12
93279382 Chain O, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 35.16 44.00 7 7 10
93279395 Chain 2, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 34.28 39.80 8 8 11
390980863 Chain T, Structure Of Yeast 20s Open-Gate Proteasome With Compound 34 24.33 31.40 6 6 10
121575 RecName: Full=78 kDa glucose-regulated protein homolog; Short=GRP-78; AltName: Full=Immunoglobulin heavy chain-binding protein homolog; Short=BiP; Flags: Precursor 24.28 11.44 5 6 8
93279392 Chain Y, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 19.31 25.47 4 4 6
403071955 Chain 2, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome 18.70 21.46 3 3 10
151941041 proteasome biogenesis-associated [Saccharomyces cerevisiae YJM789] 17.59 11.59 3 3 6
93279394 Chain 1, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 16.80 6.44 1 1 5
323353866 Ubi4p [Saccharomyces cerevisiae VL3] 15.90 54.47 3 3 5

This table pertains to Band 5 from Fig. 2 in the referenced manuscript.

Table 6.

Protein content of Band 6.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 1382.37 73.23 2 21 763
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 1239.14 73.81 3 20 651
298508455 Chain U, Proteasome Activator Complex 1003.49 73.57 2 19 352
323352352 Pre6p [Saccharomyces cerevisiae VL3] 722.91 69.05 1 17 221
417149 RecName: Full=Heat shock protein SSA1; AltName: Full=Heat shock protein YG100 201.34 59.03 8 34 61
123624 RecName: Full=Heat shock protein SSA2 194.83 55.40 5 32 58
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 160.69 79.42 20 20 63
151944720 22.6 kDa proteasome subunit [Saccharomyces cerevisiae YJM789] 131.89 47.47 9 9 49
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 105.70 46.60 8 8 31
984187 transcription factor [Saccharomyces cerevisiae] 98.23 50.64 21 21 30
312258 PUP2 [Saccharomyces cerevisiae] 84.62 56.54 14 14 26
121575 RecName: Full=78 kDa glucose-regulated protein homolog; Short=GRP-78; AltName: Full=Immunoglobulin heavy chain-binding protein homolog; Short=BiP; Flags: Precursor 83.13 29.62 14 15 22
256274381 Pba1p [Saccharomyces cerevisiae JAY291] 71.41 45.65 8 8 19
390980834 Chain S, Structure Of Yeast 20s Open-Gate Proteasome With Compound 20 50.61 62.66 10 10 16
93279393 Chain Z, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 47.35 39.64 6 6 18
93279382 Chain O, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 37.34 44.00 8 8 13
403071955 Chain 2, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome 33.68 37.16 7 7 13
390980863 Chain T, Structure Of Yeast 20s Open-Gate Proteasome With Compound 34 32.65 31.40 6 6 10
93279395 Chain 2, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 31.38 59.18 8 8 10
171457 enolase [Saccharomyces cerevisiae] 19.63 16.25 5 5 6
93279392 Chain Y, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 18.74 25.47 5 5 6
166007292 Chain E, Crystal Structure Of A Novel Chaperone Complex For Yeast 20s Proteasome Assembly 18.72 44.97 4 4 5
323353866 Ubi4p [Saccharomyces cerevisiae VL3] 13.64 54.47 3 3 4
256270485 Pdc1p [Saccharomyces cerevisiae JAY291] 11.03 9.39 2 2 3
171541 glyceraldehyde-3-phosphate dehydrogenase (G3PD) [Saccharomyces cerevisiae] 10.12 17.17 3 3 6

This table pertains to Band 6 from Fig. 2 in the referenced manuscript.

Table 7.

Protein content of Band 7.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 402.40 62.99 3 15 176
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 369.19 63.49 1 15 200
323337524 Pre9p [Saccharomyces cerevisiae Vin13] 15.59 9.09 1 1 4
323309416 Pup3p [Saccharomyces cerevisiae FostersO] 14.74 24.08 3 3 4
340707865 Chain A, Crystal Structure Of Yeast Hsp70 (BipKAR2) ATPASE DOMAIN 12.47 12.31 4 4 4
390980863 Chain T, Structure Of Yeast 20s Open-Gate Proteasome With Compound 34 12.10 14.88 3 3 4

This table pertains to Band 7 from Fig. 3 in the referenced manuscript.

Table 8.

Protein content of Band 8.

Accession Description Score Coverage # Unique Peptides # Peptides # PSMs
444302411 Chain Q, Yeast 20s Proteasome In Complex With The Vinyl Sulfone Lu112 612.56 55.12 2 12 323
323307097 Pre6p [Saccharomyces cerevisiae FostersO] 537.41 55.56 2 12 334
298508455 Chain U, Proteasome Activator Complex 417.38 53.30 2 10 130
417149 RecName: Full=Heat shock protein SSA1; AltName: Full=Heat shock protein YG100 96.44 38.01 5 17 26
123624 RecName: Full=Heat shock protein SSA2 92.78 33.18 3 16 24
256270485 Pdc1p [Saccharomyces cerevisiae JAY291] 30.17 16.67 5 5 8
93279388 Chain U, Crystal Structure Of The Yeast 20s Proteasome In Complex With Bortezomib 21.66 20.16 4 4 6
121575 RecName: Full=78 kDa glucose-regulated protein homolog; Short=GRP-78; AltName: Full=Immunoglobulin heavy chain-binding protein homolog; Short=BiP; Flags: Precursor 15.44 8.80 3 4 4
323333274 Fur1p [Saccharomyces cerevisiae AWRI796] 10.70 20.77 3 3 3

This table pertains to Band 8 from Fig. 3 in the referenced manuscript.

Acknowledgement

This work was supported by a Research Support Funds Grant from Indiana University-Purdue University Indianapolis to A.R.K.

Footnotes

Transparency document

Transparency data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2016.11.048.

Appendix A

Supplementary data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2016.11.048.

Transparency document. Supplementary material

Supplementary material

mmc1.zip (2.2MB, zip)

Appendix A. Supplementary material

Supplementary material

mmc2.zip (908KB, zip)

Reference

  • 1.Hammack L.J., Kusmierczyk A.R. Assembly of proteasome subunits into non-canonical complexes in vivo. Biochem. Biophys. Res. Commun. 2016 doi: 10.1016/j.bbrc.2016.11.024. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary material

mmc1.zip (2.2MB, zip)

Supplementary material

mmc2.zip (908KB, zip)

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