7E7B

Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine candidate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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 

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein,Collagen alpha-1(I) chainA, B, C1520Severe acute respiratory syndrome coronavirus 2Homo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: S2COL1A1
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTC2P02452
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
D,
DA [auth d],
AA [auth a],
BA [auth b],
CA [auth c],
D,
DA [auth d],
E,
EA [auth e],
F,
FA [auth f],
G,
GA [auth g],
H,
HA [auth h],
I,
IA [auth i],
J,
JA [auth j],
K,
KA [auth k],
L,
LA [auth l],
M,
MA [auth m],
N,
NA [auth n],
O,
OA [auth o],
P,
PA [auth p],
Q,
R,
S,
T,
U,
V,
W,
X,
Y,
Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VCG
Query on VCG

Download Ideal Coordinates CCD File 
FB [auth B],
XA [auth A],
YA [auth A]
2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside
C32 H60 O10
RGPBUVUVZKQNHD-YPJAPDKZSA-N
 Ligand Interaction
ELA
Query on ELA

Download Ideal Coordinates CCD File 
EB [auth B],
VA [auth A],
WA [auth A]
9-OCTADECENOIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-MDZDMXLPSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth B],
GB [auth C],
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth B],
GB [auth C],
HB [auth C],
IB [auth C],
JB [auth C],
KB [auth C],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth A],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

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