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- PDB-8vgr: Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein V... -

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Basic information

Entry
Database: PDB / ID: 8vgr
TitleCryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 5-12-18
ComponentsCapsid protein
KeywordsVIRUS / virion capsid / capsid protein / Tulane virus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological speciesTulane virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSun, C. / Jiang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI111095 United States
CitationJournal: Biomolecules / Year: 2024
Title: The 2.6 Å Structure of a Tulane Virus Variant with Minor Mutations Leading to Receptor Change.
Authors: Chen Sun / Pengwei Huang / Xueyong Xu / Frank S Vago / Kunpeng Li / Thomas Klose / Xi Jason Jiang / Wen Jiang /
Abstract: Human noroviruses (HuNoVs) are a major cause of acute gastroenteritis, contributing significantly to annual foodborne illness cases. However, studying these viruses has been challenging due to ...Human noroviruses (HuNoVs) are a major cause of acute gastroenteritis, contributing significantly to annual foodborne illness cases. However, studying these viruses has been challenging due to limitations in tissue culture techniques for over four decades. Tulane virus (TV) has emerged as a crucial surrogate for HuNoVs due to its close resemblance in amino acid composition and the availability of a robust cell culture system. Initially isolated from rhesus macaques in 2008, TV represents a novel belonging to the genus. Its significance lies in sharing the same host cell receptor, histo-blood group antigen (HBGA), as HuNoVs. In this study, we introduce, through cryo-electron microscopy (cryo-EM), the structure of a specific TV variant (the 9-6-17 TV) that has notably lost its ability to bind to its receptor, B-type HBGA-a finding confirmed using an enzyme-linked immunosorbent assay (ELISA). These results offer a profound insight into the genetic modifications occurring in TV that are necessary for adaptation to cell culture environments. This research significantly contributes to advancing our understanding of the genetic changes that are pivotal to successful adaptation, shedding light on fundamental aspects of evolution.
History
DepositionDec 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)173,8003
Polymers173,8003
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,427,971180
Polymers10,427,971180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein


Mass: 57933.172 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tulane virus / References: UniProt: B2Y6D0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tulane virus / Type: VIRUS
Details: The Tulane virus was purified from the LLC-MK2 cell line.
Entity ID: all / Source: NATURAL
Molecular weightValue: 57 MDa / Experimental value: NO
Source (natural)Organism: Tulane virus / Strain: 9-6-17
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Macaca mulatta
Virus shellDiameter: 400 nm
Buffer solutionpH: 7.4 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified virus
Specimen supportDetails: Lacey grid coated with graphene oxide / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 23 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 969
Image scansMovie frames/image: 35

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
7PHENIXmodel fitting
8Cootmodel fitting
9UCSF Chimeramodel fitting
10UCSF ChimeraXmodel fitting
12PHENIXmodel refinement
13Rosettamodel refinement
14cryoSPARCinitial Euler assignment
15cryoSPARCfinal Euler assignment
16jsprfinal Euler assignment
17cryoSPARCclassification
18jspr3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11645 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8VG6

8vg6
PDB Unreleased entry


Accession code: 8VG6 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612142
ELECTRON MICROSCOPYf_angle_d0.85816657
ELECTRON MICROSCOPYf_dihedral_angle_d6.2981646
ELECTRON MICROSCOPYf_chiral_restr0.0491872
ELECTRON MICROSCOPYf_plane_restr0.0072160

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