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- PDB-6bfu: Glycan shield and fusion activation of a deltacoronavirus spike g... -

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Basic information

Entry
Database: PDB / ID: 6bfu
TitleGlycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections
ComponentsSpike protein
KeywordsVIRAL PROTEIN / coronavirus spike glycoprotein / porcine deltacoronavirus / viral fusion protein / glycan shield
Function / homologyCoronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / Coronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / integral component of membrane / Spike protein / Spike protein
Function and homology information
Specimen sourcePorcine deltacoronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsXiong, X. / Tortorici, M.A. / Snijder, S. / Yoshioka, C. / Walls, A.C. / Li, W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / McGuire, A.T. / Rey, F.A. / Bosch, B.J. / Veesler, D.
CitationJournal: J. Virol. / Year: 2017
Title: Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections.
Authors: Xiaoli Xiong / M Alejandra Tortorici / Joost Snijder / Craig Yoshioka / Alexandra C Walls / Wentao Li / Andrew T McGuire / Félix A Rey / Berend-Jan Bosch / David Veesler
Abstract: Coronaviruses recently emerged as major human pathogens causing outbreaks of severe acute respiratory syndrome and Middle-East respiratory syndrome. They utilize the spike (S) glycoprotein anchored ...Coronaviruses recently emerged as major human pathogens causing outbreaks of severe acute respiratory syndrome and Middle-East respiratory syndrome. They utilize the spike (S) glycoprotein anchored in the viral envelope to mediate host attachment and fusion of the viral and cellular membranes to initiate infection. The S protein is a major determinant of the zoonotic potential of coronaviruses and is also the main target of the host humoral immune response. We report here the 3.5 Å resolution cryo-electron microscopy structure of the S glycoprotein trimer from the pathogenic porcine deltacoronavirus (PDCoV), which belongs to the recently identified delta genus. Structural and glycoproteomics data indicate that the glycans of PDCoV S are topologically conserved when compared with the human respiratory coronavirus HCoV-NL63 S, resulting in similar surface areas being shielded from neutralizing antibodies and implying that both viruses are under comparable immune pressure in their respective hosts. The structure further reveals a shortened S' activation loop, containing a reduced number of basic amino acids, which participates to rendering the spike largely protease-resistant. This property distinguishes PDCoV S from recently characterized betacoronavirus S proteins and suggests that the S protein of enterotropic PDCoV has evolved to tolerate the protease-rich environment of the small intestine and to fine-tune its fusion activation to avoid premature triggering and reduction of infectivity. Coronaviruses use transmembrane spike (S) glycoprotein trimers to promote host attachment and fusion of the viral and cellular membranes. We determined a near-atomic resolution cryo-electron microscopy structure of the S ectodomain trimer from the pathogenic porcine deltacoronavirus (PDCoV), which is responsible for diarrhea in piglets and has had devastating consequences for the swine industry worldwide. Structural and glycoproteomics data reveal that PDCoV S is decorated with 78 N-linked glycans obstructing the protein surface to limit accessibility to neutralizing antibodies in a way reminiscent of what has recently been described for a human respiratory coronavirus. PDCoV S is largely protease-resistant which distinguishes it from most other characterized coronavirus S glycoproteins and suggests that enteric coronaviruses have evolved to fine-tune fusion activation in the protease-rich environment of the small intestine of infected hosts.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 27, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.2Jan 24, 2018Structure modelStructure summaryaudit_author

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Assembly

Deposited unit
A: Spike protein
B: Spike protein
C: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,998171
Polyers337,5443
Non-polymers34,454168
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)73980
ΔGint (kcal/M)337
Surface area (Å2)125510

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Components

#1: Protein/peptide Spike protein / spike glycoprotein


Mass: 112514.773 Da / Num. of mol.: 3 / Source: (gene. exp.) Porcine deltacoronavirus / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A140ES81, UniProt: A0A140ESF1*PLUS
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 102 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical...
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 33 / Formula: C6H12O6
#4: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 33 / Formula: C6H12O6

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Porcine deltacoronavirus spike glycoprotein / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Porcine deltacoronavirus
Source (recombinant)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 455710 / Symmetry type: POINT

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