EMD-32736
The interface of JMB2002 Fab binds to SARS-CoV-2 Omicron Variant S
EMD-32736
Single-particle2.47 Å
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Map released: 23/03/2022
Last modified: 30/10/2024
Sample Organism:
Mus musculus,
Severe acute respiratory syndrome coronavirus 2
Sample: SARS-CoV-2 Omicron Variant S Trimer complexed with JMB2002 Fab
Fitted models: 7wrv (Avg. Q-score: 0.507)
Deposition Authors: Yin W
,
Xu Y
,
Xu P
,
Cao X
,
Wu C
,
Gu C
,
He X
,
Wang X
,
Huang S
,
Yuan Q,
Wu K,
Hu W,
Huang Z
,
Liu J,
Wang Z
,
Jia F,
Xia K
,
Liu P,
Wang X
,
Song B
,
Zheng J
,
Jiang H
,
Cheng X
,
Jiang Y
,
Deng SJ
,
Xu HE
Sample: SARS-CoV-2 Omicron Variant S Trimer complexed with JMB2002 Fab
Fitted models: 7wrv (Avg. Q-score: 0.507)
Deposition Authors: Yin W
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Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.
Yin W
,
Xu Y
,
Xu P
,
Cao X
,
Wu C
,
Gu C
,
He X
,
Wang X
,
Huang S
,
Yuan Q,
Wu K,
Hu W,
Huang Z
,
Liu J,
Wang Z
,
Jia F,
Xia K
,
Liu P,
Wang X
,
Song B
,
Zheng J
,
Jiang H
,
Cheng X
,
Jiang Y
,
Deng SJ
,
Xu HE
(2022) Science , 375 , 1048 - 1053
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(2022) Science , 375 , 1048 - 1053
Abstract:
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant infective strain. We report the structures of the Omicron spike trimer on its own and in complex with angiotensin-converting enzyme 2 (ACE2) or an anti-Omicron antibody. Most Omicron mutations are located on the surface of the spike protein and change binding epitopes to many current antibodies. In the ACE2-binding site, compensating mutations strengthen receptor binding domain (RBD) binding to ACE2. Both the RBD and the apo form of the Omicron spike trimer are thermodynamically unstable. An unusual RBD-RBD interaction in the ACE2-spike complex supports the open conformation and further reinforces ACE2 binding to the spike trimer. A broad-spectrum therapeutic antibody, JMB2002, which has completed a phase 1 clinical trial, maintains neutralizing activity against Omicron. JMB2002 binds to RBD differently from other characterized antibodies and inhibits ACE2 binding.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant infective strain. We report the structures of the Omicron spike trimer on its own and in complex with angiotensin-converting enzyme 2 (ACE2) or an anti-Omicron antibody. Most Omicron mutations are located on the surface of the spike protein and change binding epitopes to many current antibodies. In the ACE2-binding site, compensating mutations strengthen receptor binding domain (RBD) binding to ACE2. Both the RBD and the apo form of the Omicron spike trimer are thermodynamically unstable. An unusual RBD-RBD interaction in the ACE2-spike complex supports the open conformation and further reinforces ACE2 binding to the spike trimer. A broad-spectrum therapeutic antibody, JMB2002, which has completed a phase 1 clinical trial, maintains neutralizing activity against Omicron. JMB2002 binds to RBD differently from other characterized antibodies and inhibits ACE2 binding.