Designed by: Nicolas Bayer   Group: iGEM21_TU_Kaiserslautern   (2021-10-06)

SARS-CoV-2 spike protein receptor binding domain, MocloMania B4


This part codes for the receptor binding domain of the SARS-CoV-2 spike protein. These spike proteins are part of multimeric protein structures called spikes that project outwards from the virus envelope’s outer surface.[1] As one of the four viral structural proteins it is essential for the recognition, binding and entry of the virus into the host’s cells.[2] This is mediated by the receptor binding domain, located in the S1 region of the spike protein, due to its specific binding to the angiotensin-converting enzyme 2 (ACE2) located on the outer membrane of many mammalian and bird cells.[3] This binding results in a TMPRSS2 mediated proteolytic cleavage of the spike protein S2 region, exposing a viral fusion peptide and thus enabling virus entry into the host cells.[4]

size 25.1 kDa

function coding sequence

cloning position B4

plasmid backbone pAGM1299


We were able to successfully clone this basic part into its respective L0 plasmid backbone and to confirm the integrity of the L0 construct via restriction digest and gel electrophoresis, see Figure 1. Furthermore, we were able to include it into a L1 construct, proving its correct adaptation towards MoClo assembly, see Figure 2. This part has been transfected into Leishmania, but it has not yet been tested for expression and purification functionality.

  • Figure 1 | Test digest of L0 B4 parts using BsaI
    1 | pAGM1299 | 2247 + 598 bp
    2 | L0_RBD_B4 | 2247 + 675 bp
    3 | L0_mCerulean_B4 | 2247 + 720 bp
    4 | L0_mVenus_B4 | 2247 + 720 bp
    L | Thermofischer GeneRuler Plus Ladder [bp]
  • Figure 2 | Test digest of L1 constructs using HindIII
    1 | L1_sAP_Strep_RBD_Strep8His | 3792 + 3198 + 1005 bp
    2 | L1_sAP_GST_RBD_Strep8His | 3792 + 3198 + 1623 bp
    L | Thermofischer GeneRuler Plus Ladder [bp]

The MocloMania collection

This basic part is part of the MocloMania collection, the very first collection of genetic parts specifically designed and optimized for Modular Cloning assembly and recombinant protein expression in the protozoan parasite Leishmania tarentolae.

Are you trying to express complexly glycosylated proteins? Large antibody side chains? Human proteins that require accurate post-translational modification? Then Leishmania might be just the right organism for you! Leishmania tarentolae’s glycosylation patterns resemble those of human cells more closely than any other microbial expression host, while still delivering all the benefits of microbial production systems like easy transfection and cultivation.[5] So instead of relying on mammalian cell lines, try considering Leishmania as your new expression host of choice!

Our MocloMania collection will allow you to easily modify your protein of choice and make it suitable for downstream detection and purification procedures - all thanks to the help of Modular Cloning. This cloning system was first established by Weber et al. in 2011 and relies on the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequence, hereby generating four nucleotide overhangs.[6] Every basic part in our collection is equipped with a specified set of overhangs that assign it to its designated position within the reading frame. These so-called cloning positions are labelled B2-B5 from upstream to downstream. By filling all positions with the basic parts of your choice, you can easily generate variable genetic constructs that code for the fusion protein of your desire.

We furthermore provide a specifically domesticated Leishmania expression vector, named weird_plex, which will package your fusion construct into a functional transcriptional unit that is optimized for high expression in Leishmania.

The best part? Because of the type IIS restriction properties and the specifity of the generated overhangs, restriction and ligation of your construct can all happen simultaneously in a simple one-step, one-pot reaction. This will safe you a lot of time and frustration in your cloning endeavours!

Do we have your attention? In the table below you can find some basic information on how our cloning system, along with most other MoClo systems, is set up. Please feel free to check out our wiki to find more information on Leishmania and Modular Cloning as well as to understand how this basic part integrates into our part collection. See you there!

MOCLO | Important nomenclature and parameters
Level What does this level contain? antibiotic resistance Enzyme used for ligation
L0 The foundation to every MoClo construct which are basic genetic units, such as coding sequences, promoters, terminators spectinomycin BbsI
L1 Several L0 parts assembled into a functional transcriptional unit, e.g. consisting of promoter, coding region and terminator ampicillin BsaI
L2 Multiple transcriptional units added into one multi-gene construct, e.g. a protein of interest fused to a selection marker kanamycin BbsI

Sequence and Features


This basic part has been altered in its sequence in order to make it compatible with the iGEM RCF 1000 cloning standard.
In its original form, this part contains an endogenous SapI restriction site. This is because it was specifically designed to be utilized within the Modular Cloning system as established by Weber et al. in 2011, relying on BsaI and BbsI as the executive type IIS restriction enzymes.[7] This MoClo standard is a very frequently used type IIS standard, especially when it comes to plant-based expression systems.[8][9]

Because of its intended use within the MoClo system, this basic part is domesticated against BsaI and BbsI, but not against SapI. Upon registration of this part in the iGEM Registry, the endogenous SapI restriction site was disrupted via in silico introduction of a silent mutation. We decided to do this in order to increase the chance of the judges actually taking a look at this part page and not having the part overlooked due to incompatibility.

Since the part’s amino acid sequence remains unchanged, users interested in utilizing this part for type IIS loop assembly can rely on the sequence as listed on this page. For users interested in applying this basic part to their MoClo based cloning approaches, in silico reversion of the mutation might be beneficial, since SapI proved to be a valuable enzyme for confirming part insertion via restriction digest.

We highly recommend that researchers and iGEM teams utilize this basic part within the MocloMania cloning system, since it is codon optimized towards Leishmania tarentolae and may otherwise negatively influence expression yield in other organisms.

MUTATION | bp 634 - 636 | AGC → TCG

Assembly Compatibility:
  • 10
    Illegal PstI site found at 520
  • 12
    Illegal PstI site found at 520
  • 21
    Illegal BglII site found at 458
  • 23
    Illegal PstI site found at 520
  • 25
    Illegal PstI site found at 520
    Illegal NgoMIV site found at 606
  • 1000

Reference Literature

  1. Aronson JK (25 March 2020). "Coronaviruses – a general introduction". Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford.
  2. F. Li, Structure, function, and evolution of coronavirus spike proteins. Annu. Rev. Virol. 3, 237–261
  3. Shang, J., Ye, G., Shi, K. et al. Structural basis of receptor recognition by SARS-CoV-2. Nature 581, 221–224 (2020).
  4. M. Hoffmann et al., SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280.e8 (2020).
  5. Langer T, Corvey C, Kroll K, Boscheinen O, Wendrich T, Dittrich W. Expression and purification of the extracellular domains of human glycoprotein VI (GPVI) and the receptor for advanced glycation end products (RAGE) from Rattus norvegicus in Leishmania tarentolae. Prep Biochem Biotechnol. 2017 Nov 26;47(10):1008-1015. doi: 10.1080/10826068.2017.1365252. Epub 2017 Aug 31. PMID: 28857681.
  6. Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S (2011) A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE 6(2): e16765.
  7. Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S (2011) A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE 6(2): e16765.
  8. Patron, N.J., Orzaez, D., Marillonnet, S. et al., (2015), Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol, 208: 13-19.
  9., last visited 10/16/21, 19:00 ECT
functionreceptor binding to mediate viral cell entry
ligandsAngiotensin Converting Enzyme 2 (ACE2)