SARS-CoV-2 Entry Animation from Iwasa Group – a little Christmas Present to the Scientific Community

December 24, 2020
Luise Kandler

Overview

During the Corona-dominated year 2020 scientists all over the world united and gathered as much information as possible to understand the exact mechanism behind the lifecycle of SARS-CoV-2.
The main question was: how can we stop the virus from invading the human cell and causing COVID-19? A focus in the quest to answer this question, was the SARS-CoV-2 entry mechanism. The group of Janet Iwasa contributes to this ongoing research process by providing a high-quality video animation of the SARS-CoV-2 entry into the human host cell. This current version of the entry animation has already been shown on PBS News (08.12.20) and we aim to improve it with your help in 2021 (see below)!

The Entry Animation

Click this Link to see the Entry Animation on YouTube.

This entry animation is a collection of current knowledge about the SARS-CoV-2 entry mechanism. What we know at this point is that the mechanism starts with the viral approach. An individual can be infected with SARS-CoV-2 after inhaling airborne viral particles. These viruses can then travel into the airways, where they may encounter host cells of the respiratory epithelium in the trachea and lungs.

As you can read in a previous blogpost, the Spikes (teal) are Corona’s key to invade the host cell and thus of great interest in terms of vaccination and therapeutic approaches against COVID-19. The Spike protein recognizes a specific receptor on the human host cell surface, called ACE2 (purple). Usually, the Spikes are very dynamic and able to undergo opening, closing and bending movements. But after binding to ACE2, the protein is locked into its open position.  Another protein on the cell surface, called TMPRSS2 (orange), can then come along and cut the Spike protein in a specific location. These segments of the Spike protein fall away, exposing a portion of the Spike protein which was previously hidden. 

The Spike protein is then able to undergo a series of dramatic conformational changes. During the first stage, the Spike protein inserts itself into the membrane of the cell. In the second stage, segments of the Spike protein zipper back on itself, forcing the membrane of the cell and the viral membrane to fuse. After fusion, the viral RNA is deposited into the host cell, where it will direct the cell to produce more virions. This process is known as post-fusion.

The Annotation Tool

Click this Link to use the Annotation Tool.

SARS-CoV-2 Entry Animation from Iwasa Group – a little Christmas Present to the Scientific Community 1
Figure 1: Annotation tool with the animation in the center, annotations from the Iwasa Lab on the left and Comments on the right.
SARS-CoV-2 Entry Animation from Iwasa Group – a little Christmas Present to the Scientific Community 2
Figure 2: How it looks like when you hover over the video.

In January, this will be supplemented with a tool so that the knowledge about the SARS-CoV-2 entry mechanism can be discussed interactively by scientists all over the world. This online platform will serve as a basis for scientific discussion by providing an annotation tool. Scientific users can set a pin at any point of the video and comment their suggestions, criticism or questions about the mechanism and the structure depictions (see Fig. 1 for a prototype). Based on these annotations, the Iwasa Group will improve the animation of the entry process to provide an up-to-date detailed representation of this key process. The resulting entry animation is not only addressed to scientists, but it is also used for public outreach and education.

Even though the entry mechanism is not entirely understood yet, it could already be depicted in the fantastic animation of the Iwasa Group. There are still a lot of details and additional information to be found out about this process. From January on, the annotation tool therefore will provide the opportunity to discuss this mechanism publicly.

Thanks to the Iwasa Group for this Christmas present!

Merry Christmas!

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 … Continue reading Helen Ginn
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. … Continue reading Nick Pearce
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 … Continue reading Mathias Schmidt
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 … Continue reading David Briggs
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 … Continue reading Philip Wehling
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 … Continue reading Binisha Karki
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 … Continue reading Richardson Lab
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 … Continue reading Holger Theymann
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 … Continue reading Ezika Joshua Onyeka
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 … Continue reading Katharina Hoffmann
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 … Continue reading Nicole Dörfel
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, … Continue reading Pairoh Seeliger
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 … Continue reading Oliver Kippes
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 … Continue reading Luise Kandler
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 … Continue reading Ferdinand Kirsten
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 … Continue reading Kristopher Nolte
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 … Continue reading Erik Nebelung
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 … Continue reading Toyin Akinselure
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. … Continue reading Sabrina Stäb
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. … Continue reading Alexander Matthew Payne
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 … Continue reading Maximilian Edich
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 … Continue reading Agnel Praveen Joseph
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 … Continue reading Dale Tronrud
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 … Continue reading Sam Horrell
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 … Continue reading Cameron Fyfe
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 … Continue reading Tristan Croll
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 … Continue reading Gianluca Santoni
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 … Continue reading Yunyun Gao
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 … Continue reading Johannes Kaub
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 … Continue reading Andrea Thorn
More about this author

17 comments on “SARS-CoV-2 Entry Animation from Iwasa Group – a little Christmas Present to the Scientific Community”

    1. Hello Edmundo,
      Thank you for your feedback! I am sorry to inform you that the current version of the video is under the copyright of the Iwasa Group/Thorn Group and not free for all. But there will be a release of a new version soon, which will be available for everyone. We will inform everyone about the official release on our blog, once the new version is published.

      Reply

    1. Hello Jamie,
      I am sorry to inform you that the current version of the video is under the copyright of the Iwasa Group/Thorn Group and not free for all. But there will be a release of a new version soon, which will be available for everyone. We will inform everyone about the official release on our blog, once the new version is published.

      Reply

    1. Hello Arne,
      I am sorry to inform you that the current version of the video is under the copyright of the Iwasa Group/Thorn Group and not free for all. But there will be a release of a new version soon, which will be available for everyone. We will inform everyone about the official release on our blog, once the new version is published.

      Reply

  10. What is the yellow cell surface (protein)? Is the animation intended to show the yellow cell surface protein contacting the virus particle? Is that contact significant?

    What is the basis for the animation & particularly changing shape of the spike protein connecting to the cell & pulling the virus particle to the cell?

    How much of this animation is actually confirmed by repeatable observation vs. surmised indirectly from observations that don't directly show changes of protein shapes?

    Reply

Leave a Reply

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

cross