Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.
Journal, issue, pages	Science, Vol. 375, Issue 6584, Page 1048-1053, Year 2022
Publish date	Mar 4, 2022
Authors	Wanchao Yin / Youwei Xu / Peiyu Xu / Xiaodan Cao / Canrong Wu / Chunyin Gu / Xinheng He / Xiaoxi Wang / Sijie Huang / Qingning Yuan / Kai Wu / Wen Hu / Zifu Huang / Jia Liu / Zongda Wang / Fangfang Jia / Kaiwen Xia / Peipei Liu / Xueping Wang / Bin Song / Jie Zheng / Hualiang Jiang / Xi Cheng / Yi Jiang / Su-Jun Deng / H Eric Xu /
PubMed 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 ...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.
External links	Science / PubMed:35133176 / PubMed Central
Methods	EM (single particle)
Resolution	2.47 - 3.18 Å
Structure data	32679 7wp9 EMDB-32679, PDB-7wp9: SARS-CoV-2 Omicron Variant SPIKE trimer, all RBDs down Method: EM (single particle) / Resolution: 2.56 Å 32680 7wpa EMDB-32680, PDB-7wpa: SARS-CoV-2 Omicron Variant SPIKE trimer complexed with ACE2 Method: EM (single particle) / Resolution: 2.77 Å 32681 7wpb EMDB-32681, PDB-7wpb: SARS-CoV-2 Omicron Variant RBD complexed with ACE2 Method: EM (single particle) / Resolution: 2.79 Å 32682 7wpc EMDB-32682, PDB-7wpc: The second RBD of SARS-CoV-2 Omicron Variant in complexed with RBD-ACE2 Method: EM (single particle) / Resolution: 2.57 Å 32683 7wpd EMDB-32683, PDB-7wpd: SARS-CoV-2 Omicron Variant S Trimer complexed with one JMB2002 Fab Method: EM (single particle) / Resolution: 3.18 Å 32684 7wpe EMDB-32684, PDB-7wpe: SARS-CoV-2 Omicron Variant S Trimer complexed with two JMB2002 Fab Method: EM (single particle) / Resolution: 2.69 Å 32685 7wpf EMDB-32685, PDB-7wpf: SARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 Fab Method: EM (single particle) / Resolution: 2.92 Å 32736 7wrv EMDB-32736, PDB-7wrv: The interface of JMB2002 Fab binds to SARS-CoV-2 Omicron Variant S Method: EM (single particle) / Resolution: 2.47 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-CL: Unknown entry ChemComp-ZN: Unknown entry
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human) mus musculus (house mouse) lama glama (llama) Severe acute respiratory syndrome coronavirus
Keywords	VIRAL PROTEIN / RBD / SARS-CoV-2 / Omicron / S / Trimer / Fab / Antibody