Purification of His-ubiquitin Proteins from Mammalian Cells    

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In this protocol

Original research article

A brief version of this protocol appeared in:
Cancer Cell
Jan 2012


This protocol is used to purify His-tag ubiquitin conjugated protein. In this particular case, cells were transfected with His-tag ubiquitin and p53 which allowed us to purify using His-tag and reveal the WB using antibodies against p53 to see just the p53-ubiquitinate. The present protocol can be used in general for His-tag proteins expressed in mammalian cells.

Materials and Reagents

  1. EDTA free protease inhibitors (F. Hoffmann-La Roche, catalog number: 05892988001 )
  2. Proteasome inhibitor MG-132 (Calbiochem®, catalog number: 474790-5MG )
  3. Phosphate buffered saline (PBS)
  4. Tris
  5. Ni-NTA-Agarose beads (QIAGEN, catalog number: 30210 )
  6. Urea
  7. Guanidinium-HCl ( Sigma-Aldrich, catalog number: G4505-25G )
  8. Imidazole (Sigma-Aldrich, catalog number: 12399 )
  9. Triton X-100
  10. Glycerol
  11. β-mercaptoethanol
  12. SDS
  13. Bromophenol blue
  14. Lysis buffer (see Recipes)
  15. Wash buffer (see Recipes)
  16. Elution buffer (see Recipes)
  17. 4x laemmeli buffer (see Recipes)


  1. Centrifuges
  2. Sonicator
  3. Western blotting equipment
  4. Tissue culture plates
  5. 1.5 ml eppendorf tube
  6. 15 ml falcon tube


  1. Seed 1 x 106 cells on 10 cm tissue culture plates.
  2. After 8-12 h (around 40% of confluency) cells were transfect with 0.8 μg of plasmid for the His tag protein.
  3. 4 h before stop the culture add proteasome inhibitor MG-132 to a final concentration of 25 μM.
  4. 48 h after transfection aspirate the medium and wash the cells twice with pre-chilled PBS (cell can be keeping freezing on the plates at -80 °C until the day of the purification).
  5. Scrape cell with 1 ml of lysis buffer and transfer it in 1.5 ml eppendorf tube.
  6. Sonicate cells on ice twice for 10 sec with 1 min break (the sonicator probe should go under the lysate surface to avoid foaming but taking care do not touch the walls of the eppendorf tube).
  7. Spin cells 10 min at 11,000 rpm at 4 °C.
  8. Transfer the supernant in to 15 ml falcon tube and add 4 ml more of lysis buffer.
  9. Add 75 μl of Ni2+-NTA-agarose beads pre-equilibrate with lysis buffer (take 150 μl of Ni2+-NTA-agarose bead and spin 2 min at 4,000 rpm, discard the supernant and wash with 150 μl of lysis buffer four times, last time add 75 μl of lysis buffer and use).
  10. Incubate for 4 h at RT with gently agitation.
  11. Wash the beads at RT incubating 5 min with the following buffers:
    1. Once in lysis buffer.
    2. Once in wash buffer.
    3. Twice in wash buffer plus 0.1% Triton X-100 (spin 2 min at 4,000 rpm each time to recover the beads).
  12. Elute products by incubating beads in 75 μl of elution buffer for 20 min at RT with gentle agitation.
  13. Spin the beads and transfer supernant in to an eppendorf.
  14. Add 4x laemmeli buffer and boil for western blot analysis.


  1. Lysis buffer
    6 M guanidinium-HCl
    0.1 M Na2HPO4/NaH2PO4
    10 mM Tris-HCl (pH 8)
    0.005 M imidazol
    0.01 M β-mercaptoethanol
  2. Wash Buffer
    8 M urea
    0.1 M Na2HPO4/NaH2PO4
    10 mM Tris-HCl (pH 6.8)
    0.005 M imidazol
    0.01 M β-mercaptoethanol
  3. Elution buffer
    0.2 M imidazol
    0.15 M Tris-HCl (pH 6.8)
    30% glycerol
    0.72 M β-mercaptoethanol
    5% SDS
  4. 4x laemmeli buffer
    2 ml 1 M Tris-HCl (pH 6.8)
    4.0 ml 20% (w/v) SDS
    4.0 ml glycerol
    4 mg bromophenol blue
    0.2 ml 14.3 M β-mercaptoethanol


This protocol was adapted from Gajjar et al. (2012). This work was supported by INSERM, La Ligue Contre le Cancer, and RECAMO CZ.1.05/2.1.00/03.0101. M.M.C. was supported by JSPS, AXA Research Fund, and Fundacao para a Ciencia e Tecnologia of Portugal. M.G. was supported by a research fellowship from Indo-French Centre for the Promotion of Advanced Research (IFCPAR) and from the ARC.


  1. Gajjar, M., Candeias, M. M., Malbert-Colas, L., Mazars, A., Fujita, J., Olivares-Illana, V. and Fahraeus, R. (2012). The p53 mRNA-Mdm2 interaction controls Mdm2 nuclear trafficking and is required for p53 activation following DNA damage. Cancer Cell 21(1): 25-35.
  2. Xirodimas, D., Saville, M. K., Edling, C., Lane, D. P. and Lain, S. (2001). Different effects of p14ARF on the levels of ubiquitinated p53 and Mdm2 in vivo. Oncogene 20(36): 4972-4983.
Copyright: © 2012 The Authors; exclusive licensee Bio-protocol LLC.
How to cite: Illana, V. O. and Farhaeus, R. (2012). Purification of His-ubiquitin Proteins from Mammalian Cells. Bio-protocol 2(17): e258. DOI: 10.21769/BioProtoc.258.

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xiao xiao
Sun Yat-Sen University
Hi,I've read the reference-paper and have a question about 6his-ubiquitin plasmid. A number of genes can code ubiquitin unit, for example UBB and UBC. Which gene were used for the construction of plasmid ? or just 76 amino acids for one unit of ubiquitin
7/31/2018 11:04:09 AM Reply
Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

Hello Xiao

Indeed we used just one 76 aa coding gen, and the cell add an unknown number of ubiquitin His tagget to the protein. I hope this information helps to answer your question.


7/31/2018 8:39:14 AM

xiao xiao
Sun Yat-Sen University

Thank you, Vansesa

8/15/2018 12:34:19 AM

Neoletix Lab, Inc
Sorry, I have a question, when you preparing your Lysis buffer and Wash buffer, what's the pH value for the 0.1M Na2HPO4/NaH2PO4? because different pH value needs different ratio between these two reagents.
8/11/2014 1:49:22 PM Reply
Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

Hello, the pH should be 8

8/11/2014 2:10:38 PM

Neoletix Lab, Inc

Thanks Vanesa,Let me make sure for the Lysis buffer: the pH should be the same as Tris-Hcl? so the 0.1M Na2HPO4/NaH2PO4 pH should be 8 in Lysis buffer and 6.8 in Wash buffer? or both are the same pH:7.0? Please confirm.Thank you again.

8/11/2014 2:26:00 PM

Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

yes, indeed for lysis buffer pH should be 8 and for wash buffer should be 6.8. Hope you have a nice experiment!!

8/12/2014 10:05:06 AM

Neoletix Lab, Inc
In your step "9", pre-equilibrate beads with lysis buffer, the last volume should be 75ul but not 75ml.
8/11/2014 11:44:35 AM Reply
Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

yes! indeed is 75ul

8/11/2014 2:09:12 PM

Neoletix Lab, Inc

Thanks for your reply

8/11/2014 2:26:29 PM

simone bosso
Hi,I've read the reference-papers and in both of them TrisHCL concentration in Lysis and Wash Buffers is 10mM not 100mM as written above: which is the actual TrisHCL concentration?

I've another question: why is the volume of lysis buffer requested for NiNTA beads incubation (5ml) so large?

Many Many Thanks, Simone.
10/6/2013 11:37:57 AM Reply
Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

yes you are completely right! the good concentration is 10mM, im sorry for this mistake.
On the other hand 5ml is the volume that for my proteins gave the best yield

10/7/2013 6:56:00 AM

Bio-protocol Editorial Team

Per author's request, the concentration of Tris-HCl has been corrected to 10mM in the protocol.

Bio-protocol editing team

10/24/2013 11:14:49 PM

Giuseppe Bosso
University la Sapienza Rome

I have this question: in order to obtain the input (starting material/whole cell extract) can I save 15-30ul of lysate before diluting it with 4ml more of lysis buffer and beads incubation? Many Thanks
9/21/2013 8:20:11 AM Reply
Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

Hello and sorry for the delay in the answer!!. Yes you can keep 15-30ul of the lysate.

9/26/2013 7:02:36 AM

Why is the pH actually changing between lysis and washing buffer?
1/22/2013 7:59:03 AM Reply
Lin Fang
Stanford University

When pH > pI, a protein has a net negative charge. When pH < pI, a protein has a net positive charge.

In the higher pH of lysis buffer(8.0), your His-tagged protein binds to the Nickle beads strongly, but at the same time some nonspecific proteins are negatively charged and bind to the Nickle beads.

In the lower pH of washing buffer (6.8), your His-tagged protein still remain on the beads with strong affinity due to its His tag. The nonspecific proteins bound to the beads have less (if not zero) negative charges and dissociate from Nickle beads. So after washing step, the nickle beads should only bind to the His-tagged protein.

1/27/2013 7:09:13 AM

This may be a silly question, but is it the final pH of the solution that varies between buffers, or only the pH of the TRIS used?

Thanks much!
12/14/2012 11:15:28 AM Reply
Lin Fang
Department of Pediatrics, School of Medicine, Stanford University, USA

I am not the author, but let me try to answer your question: I would think it is commonly accepted that the pH is the Tris pH. As a result, the buffer ends up in the same (or similar) pH as Tris. But it is a good lab practice to always check pH of the buffer especially when it is your first time to make such buffer. Another caution is that samples you will add in the buffer does not maximize its buffer capacity, which is also done through sensibly checking pH.

12/22/2012 9:44:20 PM

Vanesa Olivares-Illana
Instituto de Física, Universidad Autónoma de San Luis Potosí

Hello and sorry for the delay in the answer.
Im agree with Lin, is commonly accepted that the pH is the Tris pH. Just one point, in the case of wash buffer you have also the component of phosphate buffer around 8, but you slowly will go down the pH (because of the explanation of Lin) of each buffer to improve the purification.

1/28/2013 8:20:27 AM