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	Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Journal, issue, pages	Science, Vol. 373, Issue 6555, Year 2021
Publish date	Aug 6, 2021
Authors	Sophie M-C Gobeil / Katarzyna Janowska / Shana McDowell / Katayoun Mansouri / Robert Parks / Victoria Stalls / Megan F Kopp / Kartik Manne / Dapeng Li / Kevin Wiehe / Kevin O Saunders / Robert J Edwards / Bette Korber / Barton F Haynes / Rory Henderson / Priyamvada Acharya /
PubMed Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike mutations enable increased transmission and antibody resistance. We combined cryo-electron microscopy (cryo- ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike mutations enable increased transmission and antibody resistance. We combined cryo-electron microscopy (cryo-EM), binding, and computational analyses to study variant spikes, including one that was involved in transmission between minks and humans, and others that originated and spread in human populations. All variants showed increased angiotensin-converting enzyme 2 (ACE2) receptor binding and increased propensity for receptor binding domain (RBD)-up states. While adaptation to mink resulted in spike destabilization, the B.1.1.7 (UK) spike balanced stabilizing and destabilizing mutations. A local destabilizing effect of the RBD E484K mutation was implicated in resistance of the B.1.1.28/P.1 (Brazil) and B.1.351 (South Africa) variants to neutralizing antibodies. Our studies revealed allosteric effects of mutations and mechanistic differences that drive either interspecies transmission or escape from antibody neutralization.
External links	Science / PubMed:34168071 / PubMed Central
Methods	EM (single particle)
Resolution	2.83 - 4.05 Å
Structure data	23546 7lwi EMDB-23546, PDB-7lwi: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Method: EM (single particle) / Resolution: 3.07 Å 23547 7lwj EMDB-23547, PDB-7lwj: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Method: EM (single particle) / Resolution: 3.24 Å 23548 7lwk EMDB-23548, PDB-7lwk: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Method: EM (single particle) / Resolution: 2.92 Å 23549 7lwl EMDB-23549, PDB-7lwl: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Method: EM (single particle) / Resolution: 2.84 Å 23550 7lwm EMDB-23550, PDB-7lwm: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation Method: EM (single particle) / Resolution: 2.83 Å 23551 7lwn EMDB-23551, PDB-7lwn: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation Method: EM (single particle) / Resolution: 2.94 Å 23552 7lwo EMDB-23552, PDB-7lwo: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation Method: EM (single particle) / Resolution: 2.85 Å 23553 7lwp EMDB-23553, PDB-7lwp: Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 2-RBD up conformation Method: EM (single particle) / Resolution: 3.01 Å 23554 7lwq EMDB-23554, PDB-7lwq: Mink Cluster 5-associated SARS-CoV-2 spike protein(S-GSAS-D614G-delFV) missing the S1 subunit and SD2 subdomain of one protomer Method: EM (single particle) / Resolution: 3.44 Å 23556 7lwt EMDB-23556, PDB-7lwt: UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.19 Å 23557 7lwu EMDB-23557, PDB-7lwu: UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.22 Å 23558 7lwv EMDB-23558, PDB-7lwv: UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.12 Å 23559 7lww EMDB-23559, PDB-7lww: Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 1-RBD-up conformation (S-GSAS-D614G-K417N-E484K-N501Y) Method: EM (single particle) / Resolution: 3.0 Å 23593 7lyk EMDB-23593, PDB-7lyk: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 2-RBD-up conformation Method: EM (single particle) / Resolution: 3.65 Å 23594 7lyl EMDB-23594, PDB-7lyl: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the RBD-down conformation Method: EM (single particle) / Resolution: 3.72 Å 23595 7lym EMDB-23595, PDB-7lym: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the RBD-down conformation Method: EM (single particle) / Resolution: 3.57 Å 23596 7lyn EMDB-23596, PDB-7lyn: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.32 Å 23597 7lyo EMDB-23597, PDB-7lyo: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.32 Å 23598 7lyp EMDB-23598, PDB-7lyp: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 4.05 Å 23599 7lyq EMDB-23599, PDB-7lyq: South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.34 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	severe acute respiratory syndrome coronavirus 2
Keywords	VIRAL PROTEIN / SARS-CoV-2 Spike Protein Trimer