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- PDB-6b3o: Tectonic conformational changes of a coronavirus spike glycoprote... -

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Basic information

Entry
Database: PDB / ID: 6b3o
TitleTectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
DescriptorSpike glycoprotein
KeywordsVIRAL PROTEIN / Coronavirus / membrane fusion / MHV / SARS / MERS
Specimen sourceMurine coronavirus / virus / MHV-A59
MethodElectron microscopy (4.1 Å resolution / Particle / Single particle)
AuthorsWalls, A.C. / Tortorici, M.A. / Snijder, J. / Xiong, X. / Bosch, B.J. / Rey, F.A. / Veesler, D.
CitationProc.Natl.Acad.Sci.Usa, 2017

Proc.Natl.Acad.Sci.Usa, 2017
Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
Walls, A.C. / Tortorici, M.A. / Snijder, J. / Xiong, X. / Bosch, B.J. / Rey, F.A. / Veesler, D.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 22, 2017 / Release: Oct 4, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 4, 2017Structure modelrepositoryInitial release
1.1Oct 18, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)198,5973
Polyers198,5973
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)36930
ΔGint (kcal/M)-287
Surface area (Å2)45680

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Components

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


Mass: 66199.094 Da / Num. of mol.: 3 / Fragment: residues 718-1252 / Source: (gene. exp.) Murine coronavirus / virus / References: UniProt: P11224
Sequence detailsThe authors state that all the differences between the sequence provided and the sequence database reference are accounted for by modifications that they made to their construct: residues 1253-1254: BiP secretion signal, residues 1253-1254: linker, residues 1255-1284: GCN4 trimerization motif, residues 1285-1290: Thrombin cleavage site, residues 1291-1300: Strep-tag

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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: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.18 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Murine hepatitis virus
Source (recombinant)Organism: Drosophila melanogaster
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Protochips C-flat
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 recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImaging IDImage processing IDFitting ID
2LeginonIMAGE ACQUISITION1
4RELION2.0.3CTF CORRECTION1
7CootMODEL FITTING1
9RELION2.0.3INITIAL EULER ASSIGNMENT1
10RELION2.0.3FINAL EULER ASSIGNMENT1
12RELION2.0.3RECONSTRUCTION1
13RosettaMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 106000 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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