7YR3

SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75.

Cao, Y.Song, W.Wang, L.Liu, P.Yue, C.Jian, F.Yu, Y.Yisimayi, A.Wang, P.Wang, Y.Zhu, Q.Deng, J.Fu, W.Yu, L.Zhang, N.Wang, J.Xiao, T.An, R.Wang, J.Liu, L.Yang, S.Niu, X.Gu, Q.Shao, F.Hao, X.Meng, B.Gupta, R.K.Jin, R.Wang, Y.Xie, X.S.Wang, X.

(2022) Cell Host Microbe 30: 1527

  • DOI: https://doi.org/10.1016/j.chom.2022.09.018
  • Primary Citation of Related Structures:  
    7YQT, 7YQU, 7YQV, 7YQW, 7YQX, 7YQY, 7YQZ, 7YR0, 7YR1, 7YR2, 7YR3

  • PubMed Abstract: 

    Recently emerged SARS-CoV-2 Omicron subvariant, BA.2.75, displayed a growth advantage over circulating BA.2.38, BA.2.76, and BA.5 in India. However, the underlying mechanisms for enhanced infectivity, especially compared with BA.5, remain unclear. Here, we show that BA.2.75 exhibits substantially higher affinity for host receptor angiotensin-converting enzyme 2 (ACE2) than BA.5 and other variants. Structural analyses of BA.2.75 spike shows its decreased thermostability and increased frequency of the receptor binding domain (RBD) in the "up" conformation under acidic conditions, suggesting enhanced low-pH-endosomal cell entry. Relative to BA.4/BA.5, BA.2.75 exhibits reduced evasion of humoral immunity from BA.1/BA.2 breakthrough-infection convalescent plasma but greater evasion of Delta breakthrough-infection convalescent plasma. BA.5 breakthrough-infection plasma also exhibits weaker neutralization against BA.2.75 than BA.5, mainly due to BA.2.75's distinct neutralizing antibody (NAb) escape pattern. Antibody therapeutics Evusheld and Bebtelovimab remain effective against BA.2.75. These results suggest BA.2.75 may prevail after BA.4/BA.5, and its increased receptor-binding capability could support further immune-evasive mutations.


  • Organizational Affiliation

    Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China. Electronic address: yunlongcao@pku.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth B],
B [auth C],
D [auth F]
1,270Severe acute respiratory syndrome coronavirus 2Mutation(s): 42 
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: 5Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2C [auth D],
E [auth G]
603Homo sapiensMutation(s): 0 
Gene Names: ACE2
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q9BYF1-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F [auth A],
G [auth E],
H,
I,
J,
F [auth A],
G [auth E],
H,
I,
J,
K,
L,
M,
N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth F]
BA [auth B]
BB [auth F]
CA [auth B]
AA [auth B],
AB [auth F],
BA [auth B],
BB [auth F],
CA [auth B],
CB [auth F],
DA [auth C],
DB [auth F],
EA [auth C],
EB [auth F],
FA [auth C],
FB [auth F],
GA [auth C],
GB [auth F],
HA [auth C],
HB [auth F],
IA [auth C],
IB [auth F],
JA [auth C],
JB [auth F],
KA [auth C],
KB [auth F],
LA [auth C],
LB [auth F],
MA [auth C],
MB [auth F],
NA [auth C],
O [auth B],
OA [auth C],
P [auth B],
PA [auth C],
PB [auth G],
Q [auth B],
QA [auth C],
QB [auth G],
R [auth B],
RA [auth C],
RB [auth G],
S [auth B],
SA [auth C],
SB [auth G],
T [auth B],
TA [auth C],
U [auth B],
V [auth B],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NB [auth G],
UA [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
OB [auth G],
VA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2022-10-19 
  • Deposition Author(s): Wang, L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2022-11-23
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary