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	Cryo-EM structures of prefusion SIV envelope trimer.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 29, Issue 11, Page 1080-1091, Year 2022
Publish date	Nov 7, 2022
Authors	Jason Gorman / Chunyan Wang / Rosemarie D Mason / Alexandra F Nazzari / Hugh C Welles / Tongqing Zhou / Julian W Bess / Tatsiana Bylund / Myungjin Lee / Yaroslav Tsybovsky / Raffaello Verardi / Shuishu Wang / Yongping Yang / Baoshan Zhang / Reda Rawi / Brandon F Keele / Jeffrey D Lifson / Jun Liu / Mario Roederer / Peter D Kwong /
PubMed Abstract	Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion ...Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion stabilization and cryo-EM structures of soluble envelope (Env) trimers from rhesus macaque SIV (SIV) in complex with neutralizing antibodies. These structures provide residue-level definition for SIV-specific disulfide-bonded variable loops (V1 and V2), which we used to delineate variable-loop coverage of the Env trimer. The defined variable loops enabled us to investigate assembled Env-glycan shields throughout SIV, which we found to comprise both N- and O-linked glycans, the latter emanating from V1 inserts, which bound the O-link-specific lectin jacalin. We also investigated in situ SIV-Env trimers on virions, determining cryo-electron tomography structures at subnanometer resolutions for an antibody-bound complex and a ligand-free state. Collectively, these structures define the prefusion-closed structure of the SIV-Env trimer and delineate variable-loop and glycan-shielding mechanisms of immune evasion conserved throughout SIV evolution.
External links	Nat Struct Mol Biol / PubMed:36344847 / PubMed Central
Methods	EM (subtomogram averaging) / EM (single particle)
Resolution	4.12 - 10.0 Å
Structure data	EMDB-25062: In-situ structure of SIV trimer Method: EM (subtomogram averaging) / Resolution: 8.5 Å EMDB-25063: in situ SIVmac239-Env trimers on the surface of AT-2-inactivated virions Method: EM (subtomogram averaging) / Resolution: 7.0 Å EMDB-25064: in situ SIVmac239-Env trimers on the surface of AT-2-inactivated virions Method: EM (subtomogram averaging) / Resolution: 7.0 Å EMDB-25065: In-situ structure of SIVmac239-Env trimers with ITS90.03 associated Method: EM (subtomogram averaging) / Resolution: 10.0 Å EMDB-27631: SIV mac239 SOS-2P K169T Env trimer with bNAb PGT145 and jacalin Method: EM (single particle) / Resolution: 7.64 Å 27718 8dua EMDB-27718, PDB-8dua: SIV E660.CR54 SOS-2P Env Trimer with ITS92.02 Method: EM (single particle) / Resolution: 4.32 Å 27735 8dvd EMDB-27735, PDB-8dvd: Cryo-EM structure of SIVmac239 SOS-2P Env trimer in complex with human bNAb PGT145 Method: EM (single particle) / Resolution: 4.12 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-MAN: alpha-D-mannopyranose / Mannose
Source	Simian-Human immunodeficiency virus Artocarpus heterophyllus (jackfruit) Influenza A virus simian immunodeficiency virus macaca mulatta (Rhesus monkey) homo sapiens (human)
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / SIV / ITS92 / HIV-1 / quaternary / HIV-2 / VIRAL PROTEIN-IMMUNE SYSTEM complex / CD4 / SOSIP / Vaccine / IMMUNE SYSTEM / VIRAL PROTEIN