EMD-36728
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state)
EMD-36728
Single-particle3.2 Å

Map released: 03/01/2024
Last modified: 15/01/2025
Sample Organism:
Homo sapiens,
Severe acute respiratory syndrome coronavirus 2
Sample: SARS-CoV-2 XBB1.5 spike glycoprotein with ACE2
Fitted models: 8jyo (Avg. Q-score: 0.337)
Deposition Authors: Yajima H
,
Anraku Y
,
Kita S
,
Kimura K,
Sasaki J,
Sasaki-Tabata K,
Maenaka K
,
Hashiguchi T
Sample: SARS-CoV-2 XBB1.5 spike glycoprotein with ACE2
Fitted models: 8jyo (Avg. Q-score: 0.337)
Deposition Authors: Yajima H





Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.
Tamura T
,
Irie T
,
Deguchi S,
Yajima H
,
Tsuda M
,
Nasser H
,
Mizuma K,
Plianchaisuk A
,
Suzuki S
,
Uriu K,
Begum MM,
Shimizu R,
Jonathan M
,
Suzuki R,
Kondo T,
Ito H,
Kamiyama A,
Yoshimatsu K
,
Shofa M,
Hashimoto R
,
Anraku Y
,
Kimura KT
,
Kita S
,
Sasaki J,
Sasaki-Tabata K,
Maenaka K
,
Nao N,
Wang L
,
Oda Y,
Ikeda T
,
Saito A
,
Matsuno K
,
Ito J
,
Tanaka S
,
Sato K
,
Hashiguchi T
,
Takayama K
,
Fukuhara T
(2024) Nat Commun , 15 , 1176 - 1176
























(2024) Nat Commun , 15 , 1176 - 1176
Abstract:
Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.
Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.