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Table 2 Potential ubiquitin-conjugated Cul3-binding proteins and their ubiquitination sites

From: Novel Cul3 binding proteins function to remodel E3 ligase complexes

Protein name

Number of residues

Accession #

Domains

Peptide sequence

Ub-sites

Charge state

Mass error (ppm)

XCorr value

Exp L2

Exp M3

Exp M4

Exp M5

Exp M6

Exp M7

Cell division/Cell cycle control

Rb1-inducible coiled coil protein 1

1594

NP_055596

No domain

LTHLGTAVSVMAK*

K201

2

12.4

2.012

1

-

-

-

-

-

    

TFVQK*EQCDFSNSLK

K828

2

19.7

2.885

-

1

-

-

-

-

Cytoskeleton

DST protein

258

AAH04912

GAS2

K*SPASKLDK

K249

2

15.5

2.055

1

-

-

-

-

-

    

SPASKLDK

none

1

18.7

2.136

1

-

-

-

-

-

    

EKFILADGASQGMAAFRPR

none

2

16.6

2.693

-

1

-

-

-

-

Filamin B

2591

BAD52434

CH, IG_FLMN

ATQTGDASK

none

1

18.6

1.584

1

-

-

-

-

-

    

ETTDFKVDTKAAGSGELGVTMK

none

2

3.9

3.121

-

1

-

-

-

-

    

SGCIVNNLAEFTVDPK*

K673

2

9.7

2.139

1

-

-

-

-

-

Hormone receptor

Thyroid hormone receptor interactor 11

1979

NP_004230

No domain

K*VAFDVK*MENEK

K670, K676

2

17.8

2.879

-

-

1

1

2

-

    

K*VAFDVKMENEK*

K670, K681

2

5.4

2.581

1

-

-

-

-

-

    

MQLLQSLQEQK

none

2

0.6

2.463

1

-

-

-

-

-

Immune system

Lymphocyte antigen 75

1722

NP_002340

FN2, CLECT

DGAICYK*PTK

K1514

2

6.6

2.182

1

-

-

-

-

-

    

DGAICYKPTK*

K1517

2

9.8

2.260

1

-

-

-

-

-

Metabolism

Aspartate beta-hydroxylase isoform a

758

NP_004309

Asp-B_Hydr, TPR, Asp-Arg-Hy

ARYGK*AQCEDDLAEK

K381

2

12.1

2.730

-

1

-

-

-

-

    

ARYGKAQCEDDLAEK*

K391

2

3.9

2.338

-

2

-

-

-

-

    

PKLLNK*FDK

K332

2

3.9

2.338

1

-

-

-

-

-

Muscle

Long myosin light chain kinase

1914

AAQ02673

S_TKc, FN3, IGcam

ESK*LDSLEAAAK

K284

2

5.0

2.382

1

-

-

-

-

-

    

ESKLDSLEAAAK*SK*

K293, K295

1

19.7

2.338

1

-

-

-

-

-

Myosin binding protein C, fast type

1141

NP_004524

FN3, IGcam

TSEKK*SDTAGELDFSGLLK*

K175, K185

3

1.4

2.821

1

-

-

-

-

-

    

TSENAIVVVAGNK*

K562

2

12.6

2.967

-

-

-

1

-

-

Nesprin-1

8797

AAN60442

CH, SPEC

SAREKGER

none

1

8.9

1.688

1

-

-

-

-

-

    

WVQYTAGKQTGIEVKDFGK*

K212

3

20.0

3.426

-

1

-

-

-

-

Neuron

Synaptojanin 2A

1288

AAN73051

Syja_N, IPPc

SSGKIFKDFHEGAINFGPTYK

none

2

0.9

2.005

1

-

-

-

-

-

    

TGMGGK*AGNKGAVGIR

K678

2

3.6

2.048

1

-

-

-

-

-

Oncoprotein

BRCA2 and CDKN1A interacting protein

322

CAI12093

No domain

AGLIQSR

none

1

9.2

1.813

1

-

-

-

-

-

    

NCEK*SMVEQLDK

K159

1

19.7

1.922

1

-

-

-

-

-

Signal transduction

Endothelial differentiation, sphingolipid G-protein-coupled receptor, 1

382

NP_001391

7tm_1

CPSGDSAGKFK*R

K340

2

6.1

2.170

1

-

-

-

-

-

    

HYNYTGK*

K34

1

14.8

1.973

1

-

-

-

-

-

Triple functional domain (PTPRF interacting) variant

2202

BAD92991

SPEC, SH3, RhoGEF, PH_TRIO

AFAAALDER

none

2

15.9

3.027

-

-

1

-

-

-

    

LVNASVAFYK*

K1003

2

1.4

2.046

1

-

-

-

-

-

Ubiquitination

Cullin3

768

NP_003581

Cullin

GVKGLTEQEVETILDK*

K414

2

11.9

2.443

1

-

-

-

-

-

Unknown function

Chromosome 10 open reading frame 92

876

AAH34223

No domain

GRKGSIPR

none

1

17.3

1.551

1

-

-

-

-

-

    

ARVQTPAVVADSGKSK

none

2

6.7

2.024

1

-

-

-

-

-

    

K*GSIPR

K233

1

1.2

1.535

1

-

-

-

-

-

KIAA1602 protein

906

AAH33253

No domain

EGAGGGSPLR

none

2

11.5

2.039

1

-

-

-

-

-

    

SKGLPK*

K62

1

3.8

1.931

1

-

-

-

-

-

RING finger and CHY zinc finger domain containing protein 1 variant

263

BAD92309

zf_CHY

DKK*QYHCENCGICR

K65

2

10.2

2.581

-

1

-

-

-

-

    

GYRCPLCMHSALDMTR

none

2

1.1

2.126

1

-

-

-

-

-

    

PYK*CMHCEK*VFR

K306, K312

2

16.4

2.036

1

-

-

-

-

-

  1. Legend:
  2. *Charge state represents the charge state of the precursor peptide ion.
  3. *Mass error (ppm; parts per million) represents the calculated mass difference between the mass of theoretical precursor peptide and the mass of the experimental precursor peptide.
  4. *Xcorr value represents the calculated value of the accuracy between the peaks of the theoretical spectra and the experimental spectra.
  5. *Ub-sites represents the position of the ubiquitin-conjugated lysine residues in a given protein.
  6. *Number of the peptides based on the corresponding mass spectra from each mass spectrometry experiment shown in Table 1 (L = long gradient; M = MudPIT).
  7. The ubiquitinated lysine residues are marked by an asterisk (*). See also Additional file1: Figure S2.