8GS6

Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant.

Saito, A.Tamura, T.Zahradnik, J.Deguchi, S.Tabata, K.Anraku, Y.Kimura, I.Ito, J.Yamasoba, D.Nasser, H.Toyoda, M.Nagata, K.Uriu, K.Kosugi, Y.Fujita, S.Shofa, M.Monira Begum, M.Shimizu, R.Oda, Y.Suzuki, R.Ito, H.Nao, N.Wang, L.Tsuda, M.Yoshimatsu, K.Kuramochi, J.Kita, S.Sasaki-Tabata, K.Fukuhara, H.Maenaka, K.Yamamoto, Y.Nagamoto, T.Asakura, H.Nagashima, M.Sadamasu, K.Yoshimura, K.Ueno, T.Schreiber, G.Takaori-Kondo, A.Shirakawa, K.Sawa, H.Irie, T.Hashiguchi, T.Takayama, K.Matsuno, K.Tanaka, S.Ikeda, T.Fukuhara, T.Sato, K.

(2022) Cell Host Microbe 30: 1540-1555.e15

  • DOI: https://doi.org/10.1016/j.chom.2022.10.003
  • Primary Citation of Related Structures:  
    8GS6

  • PubMed Abstract: 

    The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency, but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.


  • Organizational Affiliation

    Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,246Severe acute respiratory syndrome coronavirus 2Mutation(s): 46 
Gene Names: S2
UniProt
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 GroupP0DTC2
Glycosylation
Glycosylation Sites: 14Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth C]
EA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101093
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121037
Japan Science and TechnologyJapanJPMJCR20H8
Japan Society for the Promotion of Science (JSPS)JapanJPJSCCA20190008
Japan Society for the Promotion of Science (JSPS)Japan20H05773
Japan Society for the Promotion of Science (JSPS)JapanJP20H05873

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references, Refinement description, Structure summary
  • Version 1.2: 2024-10-16
    Changes: Data collection, Refinement description, Structure summary