PDBsum entry 7ad1

Viral protein

PDB id: 7ad1

Contents

Protein chains

950 a.a.

Ligands

NAG-NAG ×10

NAG ×10

PDB id:

7ad1

Name:

Viral protein

Title:

Cryo-em structure of a prefusion stabilized sars-cov-2 spike (d614n, r682s, r685g, a892p, a942p and v987p)(one up trimer)

Structure:

Spike glycoprotein,envelope glycoprotein,spike glycoprotein,envelope glycoprotein,sars-cov-2 s protein. Chain: a, b, c. Synonym: s glycoprotein,e2,peplomer protein. Engineered: yes

Source:

Severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus 1. 2019-ncov. Organism_taxid: 2697049, 11676. Gene: s, 2, s gene. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: expi293f. Expression_system_organ: kidney

Authors:

L.Rutten,L.L.R.Renault,J.Juraszek,J.P.M.Langedijk

Key ref:

J.Juraszek et al. (2021). Stabilizing the closed SARS-CoV-2 spike trimer. Nat Commun, 12, 244. PubMed id: 33431842 DOI: 10.1038/s41467-020-20321-x

Date:

14-Sep-20 Release date: 04-Nov-20

Protein chains

M1E1E4  (M1E1E4_HV1) -  Envelope glycoprotein from Human immunodeficiency virus type 1

Seq: 59 a.a.

Struc: 950 a.a.*

Protein chains

P0DTC2  (SPIKE_SARS2) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus 2

Seq: 1273 a.a.

Struc: 950 a.a.*

* PDB and UniProt seqs differ at 55 residue positions (black crosses)

DOI no: 10.1038/s41467-020-20321-x

Nat Commun 12:244 (2021)

PubMed id: 33431842

Stabilizing the closed SARS-CoV-2 spike trimer.

J.Juraszek, L.Rutten, S.Blokland, P.Bouchier, R.Voorzaat, T.Ritschel, M.J.G.Bakkers, L.L.R.Renault, J.P.M.Langedijk.

ABSTRACT

The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to prematurely refold to the post-fusion conformation, compromising immunogenic properties and prefusion trimer yields. To support ongoing vaccine development efforts, we report the structure-based design of soluble S trimers with increased yields and stabilities, based on introduction of single point mutations and disulfide-bridges. We identify regions critical for stability: the heptad repeat region 1, the SD1 domain and position 614 in SD2. We combine a minimal selection of mostly interprotomeric mutations to create a stable S-closed variant with a 6.4-fold higher expression than the parental construct while no longer containing a heterologous trimerization domain. The cryo-EM structure reveals a correctly folded, predominantly closed pre-fusion conformation. Highly stable and well producing S protein and the increased understanding of S protein structure will support vaccine development and serological diagnostics.