Our new 3D printable model of SARS-CoV-2

July 18, 2022
Dale Tronrud, Andrea Thorn and Johannes Kaub

Our goal was to create a 3D printable model of SARS-CoV-2 that is as close to the actual virus as possible, but there are a lot of confusing and contradictory descriptions of the coronavirus SARS-CoV-2 in the literature. Combing through them in order to establish a complete understanding and a clear image of the virus that causes COVID-19 is a tremendous task and as new scientific observations come to light, our conceptions are being challenged, and need for adjustments arises.

At the start of the pandemic, when there were few measurements of the novel virus, its appearance was mainly inferred from knowledge about other coronaviruses, especially the closely related SARS-CoV-1 which caused the previous SARS pandemic [1]. The Coronavirus Structural Task Force created a printable model based on those images, but since then a lot of imaging data has been collected on the new virus, itself, and those images indicate that SARS-CoV-2 is sufficiently different. We have combed the literature and used what we learned to design an updated model.

The Shape of the Virus

Because viruses are so small, it is very difficult to directly observe them even with modern imaging techniques. (For more details, see here.) In the olden days, viruses were studied by coating samples with metal and then taking an electron microscopic image (see figure) so that the surface can be clearly seen. This is, by the way, the origin of the name “coronavirus”: The viral particles looked a bit like little suns surrounded by a corona of rays of light.

Our new 3D printable model of SARS-CoV-2 1
Figure 1. a–c Slices of tomograms showing extracellular virions released from A549-ACE2, VeroE6, and Calu3 cells, respectively. d–f magnified views of (a–c), for better visualization, 10 slices were average. Unmodified picture by Klein et al., published under CC 4.0 BY (http://creativecommons.org/licenses/by/4.0/) on https://doi.org/10.1038/s41467-020-19619-7.

The most powerful ways to study the shape of a virus do not just investigate a single particle, but average the images of hundreds of them together resulting in information that does not describe a single virion but instead their average. In reality, and particularly for coronaviruses, every individual virus particle looks different, some being larger, and some smaller.  They are only perfectly round in the absence of any exterior forces or perturbing internal structure. It does not take much to deform the “wobbly" thin double membrane hull of SARS-CoV-2. For example, it has been suggested that coronavirus particles are created in a close-to-perfect spherical shape and exposure to a slightly acidic environment causes virions to become a bit deformed, a change that might be important for infectiousness, and it has been postulated that the conformation of the M proteins affects the membrane curvature and, hence, the shape of the virus [2]. Our model is therefore not exactly round but more shaped like a potato. We do not claim that this is “the shape” of the virus, but simply one of many possible shapes.

A second difference between the old and new data is that SARS-CoV-2 appears to be smaller than the other viruses studied before this pandemic. To reflect the new data we have reduced the diameter of our model by 12%, from 100 mm to 88 mm. (Our model is scaled so 1 mm corresponds to 1 nm.) As with virual shape, individual viruses have a variety of diameters and 88 mm is simply one of many sizes which are consistent with the population. Due to the adjustments to the virus body its hull surface was reduced by roughly 23%. Research suggests that M proteins are distributed on the surface of a virion with a roughly constant density so we reduced their number by a matching 23%. The data for the E protein, however, indicates a roughly constant number in each virion so we have left their number at twenty. At this scale, the RNA contained in the virion would be about 10 meters long and one mm thick. One of the models for the virion body that we supply has a hole in the bottom that, both, allows the model to sit on a table and be used as a paper weight, and allows a 10 m long piece of twine to be hidden inside. The twine can be extracted during a demonstration to emphasize the surprising length of the SARS-CoV-2 RNA molecule.

Reconsidering the Spikes

As was found for the size of the virion, the experimental data derived from direct study of SARS-CoV-2 indicates a different number of spikes per particle than seen in previous studies, and the new number is far smaller. Current literature suggests the average number of spikes on the SARS-CoV-2 viral surface ranges from 26 [3]  to 48 [4] . Our first model of SARS-CoV-2, based on images of other coronaviruses, had around 100 spikes but in our new model we have reduced their number to only 26.

While it is possible that SARS-CoV-2 does, indeed, have a different number of spikes than other coronaviruses, it is also possible that this substantial difference might well stem from changes in experimental approaches and circumstances. The microscopes and imaging techniques of today are much more powerful than those of even ten years ago.

In the past, despite the inconceivably small size of a single virion, coronavirus particles were too large to for all of its parts to be in focus in an image. Since one could only “see” the spikes in a limited region of a virus some rather elaborate methods were employed to estimate the total number of spikes. One of these is the Tammes problem, a mathematical puzzle that aims to distribute the maximum number of nonoverlapping, equal-sized circles on the surface of a sphere. Estimates for the minimal distance between two spike proteins on the viral surface are readily available even from 2D imaging, and following the assumption that the entire surface of the virion is covered with spikes packed as closely as possible the Tammes method suggests the presence of around 50 spikes per virus particle.

Our new 3D printable model of SARS-CoV-2 2
Figure 2. Webcomic by Randall Munroe, https://xkcd.com/2446.

However, many images of SARS-CoV-2 show gaps between spikes, and it is quite likely that the density of spikes is lower. New techniques applied to SARS-CoV-2 can produce a sharp image of an entire, individual particle allowing the spikes to simply be counted. These studies show an average of 26 spikes per virion and this is probably the most reasonable estimate available until further experimental evidence emerges. This is just an average; the exact number of spikes on a particular virion varies around that value. The same publication also states that spikes are able to rotate freely on the viral surface and are not standing entirely upright, but are instead inclined by 40° on average [3], again varying a lot from spike to spike. Our updated version of the SARS-CoV-2 model incorporates these new findings. It has 26 spikes whose stalks are bent at angles of 30°, 40° and 50°. To improve the model’s flexibility and sturdiness, we also produced a version where the spike tops are connected to the body via springs. However, enthusiasts should remember that the spike proteins (as well as membrane and envelope proteins) are also “swimming” in the bilipidic membrane that serves as the outer hull, which we could not represent in our model.

Our new 3D printable model of SARS-CoV-2 3
Fig. 3. Complete printed, painted and assembled SARS-CoV-2 spring model, with human antibody (orange) and rhinovirus (blue) at the same scale.

Now, where’s the Model?

We made the updated files for the 3D-printable virus model available on thingiverse.

In this blog article you can find detailed construction guidance for the new model.

And here's a 3D preview of the new model on Sketchfab:


[1] "Coronavirus never before seen in humans is the cause of SARS". United Nations World Health Organization. 2003-04-16. Archived from the original on 2004-08-12. Retrieved 2022-02-17.

[2] Neuman, B., Kiss, G., Kunding, A. H. et al. A structural analysis of M protein in coronavirus assembly and morphology. J. Struct. Biol. 174, 1 (2011), 11–22. https://dx.doi.org/10.1016%2Fj.jsb.2010.11.021.

[3] Yao, H., Song, Y., Chen, Y. et al. Molecular Architecture of the SARS-CoV-2 Virus. Cell 183, 3 (2020), 730-738. https://doi.org/10.1016/j.cell.2020.09.018.

[4] Klein, S., Cortese, M., Winter, S.L. et al. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun 11, 5885 (2020). https://doi.org/10.1038/s41467-020-19619-7.

Corinna the Corona Cactus

Corinna works as an outreach person for all plant-related business and as a mascot. She gathered previous experience in the garden center, and even though she can be a bit spiky, she likes to cuddle and lie in the sun.
More about this author

Helen Ginn

Senior Research Scientist @ Diamond Light Source, Oxfordshire, UK
Dr Helen Ginn is a senior research scientist at Diamond Light Source in the UK and a computational methods developer in structural biology. She is currently working on Representation of Protein Entities (RoPE) for structural biologists to interpret subtle conformational changes in dynamic protein systems. She has developed Vagabond for torsion angle-driven model refinement and […]
More about this author

Nick Pearce

Assistant Professor @ SciLifeLab DDLS Fellow
Nick obtained his undergraduate degree in Physics from the University of Oxford in 2012, and then his PhD in Systems Approaches to Biomedical Sciences in 2016. He moved to Utrecht in the Netherlands in 2017 to work with Piet Gros, where he obtained an EMBO long-term fellowship and worked on analysing disorder in macromolecular structures. […]
More about this author

Mathias Schmidt

Molecular Life Sciences M.Sc. Student @ Hamburg University
Mathias is currently doing his Master's degree in Molecular Life Sciences at the University of Hamburg and has been an auxiliary scientist in the Corona Structural Taskforce since March 2022. There he is working on the question of the origin of SARS-CoV-2. His undergraduate research focuses on the development of synthetic molecular mechanisms to regulate […]
More about this author

David Briggs

Principal Laboratory Research Scientist @ Francis Crick Institute in London, UK
David Briggs is a Principal Laboratory Research Scientist in the Signalling and Structural Biology lab at the Francis Crick Institute in London, UK. A crystallographer by training, his work focuses on the biophysical and structural characterisation of human extracellular proteins involved in the synapse, which have important ramifications in both psychiatric and neurodegenerative disorders. He […]
More about this author

Lisa Schmidt

Web Developer and Illustrator @ Mullana
Lisa Schmidt is a freelance illustrator who studied Multimedia and Communication (BA) in Ansbach, Germany. Her work is focused on visualising topics around science and technology. She joined the Coronavirus Structural Task Force as media designer, where she does web design, 3D rendering for scientific illustrations and outreach work.
More about this author

Philip Wehling

Nanosciences M.Sc. Student @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Philip has long had an enthusiasm for biological processes which is paired with an analytical understanding of the world. After having worked for a long time as a registered nurse in various fields, he first studied mathematics and finally nanosciences. During a lecture series in preparation for a bachelor's thesis, he came into contact with […]
More about this author

Binisha Karki

Postdoctoral Research Associate @ BioNTech SE
Binisha works as a research associate at BioNTech where she works on the development of COVID-19 vaccine and cancer immunotherapies. She graduated as a Molecular Biology major from Southeastern Louisiana University in May 2019. Post-graduation she worked as a research technician in the Chodera Lab performing biophysical measurements of model protein-ligand systems for computational chemistry […]
More about this author

Binisha Karki

Wissenschaftliche Mitarbeiterin @ BioNTech SE
Binisha ist als wissenschaftliche Mitarbeiterin bei BioNTech angestellt und arbeitet an der Entwicklung von Impfstoffen gegen COVID-19 sowie Krebsimmuntherapien. Sie beendete ihr Studium der Molekularbiologie an der Southeastern Louisiana University im Mai 2019. Anschließend arbeitete sie als Forschungstechnikerin im Chodera-Lab, wo sie biophysikalische Messungen an Modellen von Protein-Liganden-Systeme für computerchemische Benchmarks durchführte.
More about this author

Hauke Hillen

Assistant Professor at the University Medical Center Göttingen & Group Leader at the MPI for Biophysical Chemistry @ University Medical Center Göttingen
Hauke ist Biochemiker und Strukturbiologe. Mit seinem Forschungsteam untersucht er mittels Röntgenkristallografie und Kryo-Elektronenmikroskopie die Struktur und Funktion von molekularen Maschinen, die für die Genexpression in eukaryotischen Zellen verantwortlich sind. Er interessiert sich dabei besonders dafür wie genetisches Material außerhalb des Zellkerns exprimiert wird, zum Beispiel in menschlichen Mitochondrien oder durch Viren im Zytoplasma.
More about this author

Richardson Lab

Richardson Lab @ Duke University, Durham, North Carolina, USA
The long-term goal of the Richardson lab is to contribute to a deeper understanding of the 3D structures of proteins and RNA, including their description, determinants, folding, evolution, and control. Their approaches include structural bioinformatics, macromolecular crystallography, molecular graphics, analysis of structures, and methods development, currently focussed on the improvement of structural accuracy. In this […]
More about this author

Holger Theymann

Agile Leadership Coach @ mehr-Freu.de GmbH
Holger keeps websites running. He makes data from scientific databases appear in nice tables. He also has an eye on keeping the sites fast, safe and reliable. His experience as a software developer, systems architect, agile project manager and coach enabled the Task Force to get the whole process well organized and he even taught […]
More about this author

Florens Fischer

Biology M.Sc. Student @ Rudolf Virchow Center, Würzburg University
Florens is studying biology (M.Sc.) and worked in the Task Force as a student assistant. He has focused on bioinformatics and supports the work on automation of scripts and structuralization of big data with machine learning. He also supported the team in other areas, such as scientific research.
More about this author

Ezika Joshua Onyeka

Public Health M.Sc. student @ Hamburg University of Applied Sciences
Joshua joined Thorn Lab as a student assistant. He is a Public Health practitioner, holds a bachelor's degree in Public Health and is currently enrolled at Hamburg University of Applied Sciences for his MPH. He has helped in implementing some vaccination programmes to improve immunisation coverage and training of immunisation frontline health workers. For the […]
More about this author

Katharina Hoffmann

Molecular Biology M.Sc. student @ Institut für Nanostruktur und Festkörperphysik, Universität Hamburg
Katharina worked as a student assistant at Thorn Lab. Normally, she studies molecular biology at the University of Hamburg. In her master's thesis, which was put on hold by Corona, she is working on the interruption of bacterial communication. Since the lockdown, she has been digging around in databases and analyzing sequences. She never thought […]
More about this author

Nicole Dörfel

Media Designer @
Nicole Dörfel ensures that we and our work are looking good! She is the illustrator, media designer and the artistic soul of the Task Force. She works her magic both in print and digitally—her focus is general media design. In the Task Force, she is mainly responsible for graphics, photo editing, design of all our […]
More about this author

Pairoh Seeliger

Administration Assistant @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Pairoh Seeliger is the admin wizard of the Task Force. She takes care of media requests, handles any logistical issues that come up and makes sure our science doesn’t sound too complicated in our German outreach efforts. She self-describes as "a jack of all trades with a University education in German studies and business administration, […]
More about this author

Oliver Kippes

Biochemistry B.Sc. Student @ Rudolf Virchow Center, Würzburg University
Oli is studying biochemistry (B.Sc) and has completed a training as an IT specialist prior to his studies. With the combined knowledge of his studies and training, he helps maintaining the structural database, programs applications for it and supports the team in literature research. In spite of his study, structural biology was still a new […]
More about this author

Luise Kandler

Biochemistry B.Sc. Student @ Rudolf-Virchow Center, Würzburg University
Luise is a B.Sc. student in biochemistry at the University of Würzburg and joined the Task Force during the first Corona lockdown. She did her bachelor's thesis with the Thorn Lab, where she learned programming with Python and worked on the implementation of a GUI for our machine learning tool HARUSPEX in Coot. In the […]
More about this author

Ferdinand Kirsten

Biochemistry B.Sc. Student @ Rudolf Virchow Center, Würzburg University
Ferdinand did his bachelor's thesis at Thorn Lab on solvent exchange and interactions in macromolecular crystallography. Still new to the world of crystallography and structural refinement, he tries to help wherever he can, with a main focus on literature and genome research as well as structural refinement with Coot. Even if he's more of the […]
More about this author

Kristopher Nolte

Biochemistry B.Sc. Student @ Rudolf-Virchow Center, Würzburg University
Kristopher joined Thorn Lab as part of his bachelor thesis. In this thesis he refined aspects of the diagnostic tool for graphical X-Ray data analysis (AUSPEX) with the help of machine learning. But since the corona crisis halted all our lives, he contributes to the Task Force by using his knowledge of bioinformatics and programming […]
More about this author

Erik Nebelung

Nanoscience M.Sc. Student @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Erik is studying nanoscience with a focus on biochemical methods and applications. From August 2020 till January 2021 he pursued his studies at the iNano institute in Aarhus, before starting his master's thesis back in Hamburg. He had his first taste of protein crystallization during his bachelor's thesis work and this sparked his interest in […]
More about this author

Toyin Akinselure

Nanoscience M.Sc. Student @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Toyin ist a microbiologist and presently an M.Sc. student in nanoscience with a focus on nanobiology and nanochemistry. She is interested in scientific research especially in protein chemistry and drug discovery. In the previous autumn and winter, she interned with two research projects, one in drug discovery and the other in protein structure. She found […]
More about this author

Lea von Soosten

Physics M.Sc. Student @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Lea is a M.Sc. physics student with a great interest in everything related to biology. Even though she comes from a different field, she joined the team to expand her knowledge in biochemistry and help the Task Force with a main focus on literature research. Also, she loves drawing!
More about this author

Sabrina Stäb

Biotechnology M.Sc. Student @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Sabrina is studying biochemistry (M.Sc.) and works as a research assistant for the Thorn Lab and the CSTF. During her bachelor thesis on "Crystallization and Structure Solution of High-Quality Structures for MAD Experiments", she was able to gain a lot of experience in the field of crystallography and now brings this experience to the project. […]
More about this author

Alexander Matthew Payne

Chemical Biology Ph.D. Student @ Chodera Lab, Memorial Sloan Kettering Center for Cancer Research, New York, U.S.
Alex is a Ph.D. student interested in understanding how proteins move! He has recently joined the labs of John Chodera and Richard Hite to work on a joint project involving molecular dynamics and Cryo-EM. His goal is to generate conformational ensembles from Cryo-EM data and simulate the ensemble using massive scale molecular dynamics via Folding@Home. […]
More about this author

Maximilian Edich

Bioinformatics Ph.D. Student @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Max studied bioinformatics and genome research in Bielefeld and joined the CSTF as a Ph.D. student in 2021. Previously, his focus was on molecular modeling. Now, he works on the so-called R-factor gap. He already learned what it is like to be part of a young, scientific team as a member of the iGEM contest […]
More about this author

Agnel Praveen Joseph

Computational Scientist @ Science and Technology Facilities Council, UK
Dr. Agnel Praveen works as a computational scientist in the CCP-EM team at the Science and Technology Facilities Council, UK. He is interested in approaches to interpret and validate maps and atomic models derived from Cryo-EM data and looks also into computational methods for the interpretation of Cryo-ET data. In collaboration with five other sites […]
More about this author

Dale Tronrud

Research Scientist @
Dale Tronrud has both solved protein crystal structures and developed methods and software for the optimization of macromolecular models against X-ray data and known chemical structural information. He has had a long-standing interest in enzyme:inhibitor complexes and photosynthetic proteins, focusing on the Fenna-Matthews-Olson protein. In addition, he has also been involved in the validation and […]
More about this author

Sam Horrell

Beamline Scientist @ Diamond Light Source, Oxfordshire, UK
Sam is a structural biologist working on method development around structural biology at Diamond Light Source, in particular for ways of better understanding how enzymes function through the production of structural movies. Sam is working through deposited structures related to SARS-CoV and SARS-CoV-2 with a view to providing the most accurate protein structures possible for […]
More about this author

Cameron Fyfe

Postdoctoral Research Associate @ Micalis Institute, INRAE, Paris, France
Cameron is a structural biologist who has worked extensively on proteins from microorganisms. With many years of experience in the pharmaceutical industry and in structural biology research, he joined the Task Force to contribute his skills to improve existing models for drug development. He is currently researching Radical SAM enzymes at INRAE. When not in […]
More about this author

Tristan Croll

Postdoctoral Research Associate @ Cambridge Institute for Medical Research, University of Cambridge
Tristan is a specialist in the modelling of atomic structures into low-resolution crystallographic and cryo-EM density, and developer of the model-building package ISOLDE. His focus in the project is on correcting the various errors in geometry and/or chemical identity that tend to occur in less well-resolved regions, with the overall aim of bringing the standards […]
More about this author

Gianluca Santoni

Serial Crystallography Data Scientist @ European Synchrotron Radiation Facility, Grenoble, France
Gianluca is an expert in protein crystallography data collection and analysis. After a PhD in structure-based drug design, he has worked as a postdoc on the beamline ID23-1 at the European Synchrotron Radiation Facility (ESRF) and has developed the SSX data analysis software ccCluster. His current interests are the optimization of data collection strategies for […]
More about this author

Yunyun Gao

Postdoctoral Research Associate in the AUSPEX Project @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Yunyun is a method developer for strategies of analysing data from biomacromolecules. Before joining the Thorn group, he had been working on SAXS/WAXS of polymers and proteins. He is interested in improving objectivity and reliability of data analysis. Yunyun is currently extending the functionality of AUSPEX. He is the repository manager and AUSPEX handler for […]
More about this author

Johannes Kaub

Scientific Coordinator @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Johannes Kaub studied chemistry at RWTH Aachen, with a focus on solid-state physical chemistry, before serving as a scientific employee at the Max Planck Instiute for the Structure and Dynamics of Matter. He supports the Coronavirus Structural Task Force as a scientific coordinator with his organizing ability and his talent for solving problems. Other than […]
More about this author

Andrea Thorn

Group Leader @ Institute for Nanostructure and Solid-State Physics, Hamburg University
Andrea is a specialist for crystallography and Cryo-EM structure solution, having contributed to programs like SHELX, ANODE and (a little bit) to PHASER in the past. Her group develops the diffraction diagnostics tool AUSPEX, a neural network for secondary structure annotation of Cryo-EM maps (HARUSPEX) and enables other scientists to solve problem structures. Andrea is […]
More about this author

Leave a Reply

Your email address will not be published. Required fields are marked *