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	A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 8449, Year 2025
Publish date	Sep 26, 2025
Authors	Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli Coulibaly / Paul Young / Roy A Hall / Jody Hobson-Peters / Naphak Modhiran / Daniel Watterson /
PubMed Abstract	Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. ...Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. Here we use a chimeric virus platform to resolve the first high resolution cryo-EM structures of YFV. Stark differences in particle morphology and homogeneity are observed between vaccine and virulent strains of YFV, and these are found to have significant implications on antibody recognition and neutralisation. We identify a single residue (R380) in the YFV envelope protein that stabilises the virion surface, and leads to reduced exposure of the cross-reactive fusion loop epitope. The differences in virion morphology between YFV strains also contribute to the reduced sensitivity of the virulent YFV virions to vaccine-induced antibodies. These findings have significant implications for YFV biology, vaccinology and structure-based flavivirus antigen design.
External links	Nat Commun / PubMed:41006244 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.66 - 21.8 Å
Structure data	EMDB-44278: Chimeric flavivirus between BinJV and YFV-17D Method: EM (single particle) / Resolution: 7.5 Å EMDB-44279: Chimeric flavivirus between BinJV and YFV-ES504 Method: EM (single particle) / Resolution: 12.6 Å EMDB-44280: Chimeric flavivirus between BinJV and YFV-17D in complex with 2C9 Fab Method: EM (single particle) / Resolution: 7.3 Å EMDB-44281: Chimeric flavivirus between BinJV and YFV-ES504 in complex with 2C9 Fab Method: EM (single particle) / Resolution: 21.8 Å EMDB-44282: Chimeric flavivirus between BinJV and YFV-17D in complex with 5A Fab Method: EM (single particle) / Resolution: 11.8 Å EMDB-44283: Chimeric flavivirus between BinJV and YFV-ES504 in complex with 5A Fab Method: EM (single particle) / Resolution: 15.5 Å EMDB-44284: Chimeric flavivirus between BinJV and YFV-ES504 with YFV-17D DIII Method: EM (single particle) / Resolution: 6.5 Å EMDB-44285: Chimeric flavivirus between BinJV and YFV-ES504 with YFV-17D DIII in complex with 2C9 Fab Method: EM (single particle) / Resolution: 8.1 Å EMDB-44286: Chimeric flavivirus between BinJV and YFV-Asibi with YFV-17D DIII Method: EM (single particle) / Resolution: 5.5 Å EMDB-44287: Chimeric flavivirus between BinJV and YFV-ES504 T380R Method: EM (single particle) / Resolution: 5.7 Å 44288 9b6u EMDB-44288, PDB-9b6u: Envelope protein ASU of YFV-17D in complex with 2C9 Fab Method: EM (single particle) / Resolution: 4.0 Å 44289 9b6v EMDB-44289, PDB-9b6v: Envelope protein ASU of YFV-ES504 with YFV-17D DIII Method: EM (single particle) / Resolution: 3.3 Å 44290 9b6w EMDB-44290, PDB-9b6w: Envelope protein ASU of YFV-ES504 with YFV-17D DIII in complex with 2C9 Fab Method: EM (single particle) / Resolution: 3.6 Å 44291 9b6x EMDB-44291, PDB-9b6x: Envelope protein ASU of YFV-Asibi with YFV-17D DIII Method: EM (single particle) / Resolution: 3.6 Å 44292 9b6y EMDB-44292, PDB-9b6y: Envelope protein ASU of YFV-ES504 T380R Method: EM (single particle) / Resolution: 3.3 Å EMDB-49804: Chimeric flavivirus between BinJV and YFV-Asibi Method: EM (single particle) / Resolution: 12.5 Å EMDB-49805: Chimeric flavivirus between BinJV and YFV-Asibi T380R Method: EM (single particle) / Resolution: 8.6 Å PDB-9b8g: 2C9 Fab antibody fragment against the E protein of the Yellow Fever virus Method: X-RAY DIFFRACTION / Resolution: 2.66 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-CL: Unknown entry ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER
Source	mus musculus (house mouse) yellow fever virus homo sapiens (human)
Keywords	VIRUS/IMMUNE SYSTEM / Flavivirus / Envelope protein / Yellow fever virus / Fab / VIRUS / VIRUS-IMMUNE SYSTEM complex / IMMUNE SYSTEM / Antibody / Yellow Fever