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- PDB-5wrg: SARS-CoV spike glycoprotein -

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Basic information

Entry
Database: PDB / ID: 5wrg
TitleSARS-CoV spike glycoprotein
DescriptorSpike glycoprotein
KeywordsVIRUS LIKE PARTICLE / SARS-CoV / Receptor binding / Membrane fusion / VIRAL PROTEIN
Specimen sourceHuman SARS coronavirus / virus / SARS-CoV
MethodElectron microscopy (4.3 Å resolution / Particle / Single particle)
AuthorsGui, M. / Song, W. / Xiang, Y. / Wang, X.
CitationCell Res., 2017, 27, 119-129

Cell Res., 2017, 27, 119-129 Yorodumi Papers
Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding.
Miao Gui / Wenfei Song / Haixia Zhou / Jingwei Xu / Silian Chen / Ye Xiang / Xinquan Wang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 1, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Apr 5, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)401,0323
Polyers401,0323
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)15420
ΔGint (kcal/M)-47
Surface area (Å2)113350

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Components

#1: Polypeptide(L)Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 133677.312 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1-1196 / Source: (gene. exp.) Human SARS coronavirus / virus / References: UniProt: P59594

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: SARS-CoV spike glycoprotein / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: SARS coronavirus
Source (recombinant)Organism: Spodoptera frugiperda / Plasmid: pFastBac-Dual
Buffer solutionpH: 7.2
SpecimenEmbedding 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 FIELD
Image recordingAverage exposure time: 8 sec. / Electron dose: 4.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
4CTFFind4CTF CORRECTION1
10RELION1.4FINAL EULER ASSIGNMENT1
12RELION1.4RECONSTRUCTION1
13PHENIXMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 34152 / Symmetry type: POINT

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