Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 523.12 kDa 
• Atom Count: 26509 
• Modelled Residue Count: 3240 
• Deposited Residue Count: 4560 
• Unique protein chains: 1

7E7D

Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate

• PDB DOI: 10.2210/pdb7E7D/pdb
• EM Map EMD-30999: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2021-02-25 Released: 2021-03-24 
• Deposition Author(s): Zheng, S., Ma, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19.

Ma, J., Su, D., Sun, Y., Huang, X., Liang, Y., Fang, L., Ma, Y., Li, W., Liang, P., Zheng, S.

(2021) J Virol 

• PubMed: 33692215 
• DOI: 10.1128/JVI.00194-21
• Primary Citation of Related Structures:  
  7E7B, 7E7D


• PubMed Abstract: 
  

Within a year after its emergence, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people worldwide with a death toll over 2 million. Vaccination remains the best hope to ultimately put this pandemic to an end. Here, using Trimer-Tag technology, we produced both wild-type (WT) and furin site mutant (MT) S-Trimers for COVID-19 vaccine studies. Cryo-EM structures of the WT and MT S-Trimers, determined at 3.2 Å and 2.6 Å respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. The tightly closed conformation is stabilized by fatty acid and polysorbate 80 binding at the receptor binding domains (RBDs) and the N terminal domains (NTDs) respectively. Additionally, we identified an important pH switch in the WT S-Trimer that shows dramatic conformational change and accounts for its increased stability at lower pH. These results validate Trimer-Tag as a platform technology in production of metastable WT S-Trimer as a candidate for COVID-19 subunit vaccine. IMPORTANCE Effective vaccine against SARS-CoV-2 is critical to end the COVID-19 pandemic. Here, using Trimer-Tag technology, we are able to produce stable and large quantities of WT S-Trimer, a subunit vaccine candidate for COVID-19 with high safety and efficacy from animal and Phase 1 clinical trial studies. Cryo-EM structures of the S-Trimer subunit vaccine candidate show that it predominately adopts tightly closed pre-fusion state, and resembles that of the native and full-length spike in detergent, confirming its structural integrity. WT S-Trimer is currently being evaluated in global Phase 2/3 clinical trial. Combining with published structures of the S protein, we also propose a model to dissect the conformation change of the spike protein before receptor binding.

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Organizational Affiliation: 

Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Collagen alpha-1(I) chain	A, B, C	1520	Severe acute respiratory syndrome coronavirus 2, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: S, 2, COL1A1
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens) Explore P02452  Go to UniProtKB:  P02452
PHAROS:  P02452
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
UniProt Groups	P0DTC2P02452

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth d], BA [auth e], CA [auth f], D, DA [auth g], E, EA [auth h], F, FA [auth i], G, GA [auth j], H, HA [auth k], I, IA [auth l], J, K, L, M, N, O, P, Q [auth R], R [auth S], S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth c]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ELA	OA [auth A], PA [auth A], RA [auth B]	9-OCTADECENOIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-MDZDMXLPSA-N
NAG	AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], QA [auth A], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-02-25 
• Released Date: 2021-03-24 
Deposition Author(s): Zheng, S., Ma, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release