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

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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
Specimen sourcePorcine deltacoronavirus / virus
MethodElectron microscopy (3.5 Å resolution / Particle / Single particle) / Transmission electron microscopy
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.
CitationJ. Virol., 2017

J. Virol., 2017 Yorodumi Papers
Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections.
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

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

Structure visualization

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

Theoretical massNumber of molelcules
Total (without water)371,998171

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


#1: Protein/peptide Spike protein / spike glycoprotein

Mass: 112514.773 Da / Num. of mol.: 3 / Source: (gene. exp.) Porcine deltacoronavirus / virus / Production host: Drosophila melanogaster / References: UniProt: A0A140ES81
#2: Chemical...

Mass: 221.208 Da / Num. of mol.: 102 / Formula: C8H15NO6 / : N-Acetylglucosamine
#3: Chemical...

Mass: 180.156 Da / Num. of mol.: 33 / Formula: C6H12O6 / : Mannose
#4: Chemical...

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

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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 FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


EM software
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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