7YR3 | pdb_00007yr3

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

PDB DOI: https://doi.org/10.2210/pdb7YR3/pdb
EM Map EMD-34044: EMDB EMDataResource

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

Deposited: 2022-08-08 Released: 2022-10-19
Deposition Author(s): Wang, L.
Funding Organization(s): Not funded

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 1.4 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

PubMed: 36270286 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.chom.2022.09.018
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 579.09 kDa
Atom Count: 35,899
Modeled Residue Count: 4,400
Deposited Residue Count: 5,016
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth C], D [auth F]	1,270	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 42 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth B] Focus chain B [auth C] Focus chain D [auth F]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	C [auth D], E [auth G]	603	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C [auth D] Focus chain E [auth G]	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	2		N-Glycosylation	Interactions Focus chain F [auth A] Focus chain G [auth E] Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain F [auth A] Focus chain G [auth E] Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth C] SDF format, chain PB [auth G] SDF format, chain R [auth B] SDF format, chain RB [auth G] SDF format, chain S [auth B] SDF format, chain SB [auth G] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain WA [auth D] SDF format, chain U [auth B] SDF format, chain TA [auth C] SDF format, chain T [auth B] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QB [auth G] SDF format, chain QA [auth C] SDF format, chain Q [auth B] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MB [auth F] SDF format, chain MA [auth C] SDF format, chain LB [auth F] SDF format, chain LA [auth C] SDF format, chain KB [auth F] SDF format, chain KA [auth C] SDF format, chain JB [auth F] SDF format, chain JA [auth C] SDF format, chain IB [auth F] SDF format, chain IA [auth C] SDF format, chain HB [auth F] SDF format, chain HA [auth C] SDF format, chain FB [auth F] SDF format, chain FA [auth C] SDF format, chain DB [auth F] SDF format, chain CB [auth F] SDF format, chain BB [auth F] SDF format, chain AA [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RB [auth G] MOL2 format, chain S [auth B] MOL2 format, chain SB [auth G] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QB [auth G] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain MA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain LA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain KA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain JA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain IA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain AA [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain PB [auth G] mmCIF format, chain R [auth B] mmCIF format, chain RB [auth G] mmCIF format, chain S [auth B] mmCIF format, chain SB [auth G] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QB [auth G] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MB [auth F] mmCIF format, chain MA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain LA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain KA [auth C] mmCIF format, chain JB [auth F] mmCIF format, chain JA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain IA [auth C] mmCIF format, chain HB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain CB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain AA [auth B]	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		Interactions Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth B] Focus chain BB [auth F] Focus chain CA [auth B] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain O [auth B] Focus chain OA [auth C] Focus chain P [auth B] Focus chain PA [auth C] Focus chain PB [auth G] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain QB [auth G] Focus chain R [auth B] Focus chain RA [auth C] Focus chain RB [auth G] Focus chain S [auth B] Focus chain SA [auth C] Focus chain SB [auth G] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth B] Focus chain BB [auth F] Focus chain CA [auth B] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain O [auth B] Focus chain OA [auth C] Focus chain P [auth B] Focus chain PA [auth C] Focus chain PB [auth G] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain QB [auth G] Focus chain R [auth B] Focus chain RA [auth C] Focus chain RB [auth G] Focus chain S [auth B] Focus chain SA [auth C] Focus chain SB [auth G] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain NB [auth G] SDF format, chain UA [auth D] MOL2 format, chain NB [auth G] MOL2 format, chain UA [auth D] mmCIF format, chain NB [auth G] mmCIF format, chain UA [auth D]	NB [auth G], UA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain NB [auth G] Focus chain UA [auth D] Interactions & Density Focus chain NB [auth G] Focus chain UA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain VA [auth D] SDF format, chain OB [auth G] MOL2 format, chain VA [auth D] MOL2 format, chain OB [auth G] mmCIF format, chain VA [auth D] mmCIF format, chain OB [auth G]	OB [auth G], VA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain OB [auth G] Focus chain VA [auth D] Interactions & Density Focus chain OB [auth G] Focus chain VA [auth D]