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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
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / Coronavirus / membrane fusion / MHV / SARS / MERS
Function / homologyCoronavirus S2 glycoprotein / Spike receptor binding domain superfamily / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / host cell Golgi apparatus / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Coronavirus S2 glycoprotein / Spike receptor binding domain superfamily / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / host cell Golgi apparatus / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / pathogenesis / virion membrane / integral component of membrane / identical protein binding / Spike glycoprotein
Function and homology information
Specimen sourceMurine coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsWalls, A.C. / Tortorici, M.A. / Snijder, J. / Xiong, X. / Bosch, B.J. / Rey, F.A. / Veesler, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion.
Authors: Alexandra C Walls / M Alejandra Tortorici / Joost Snijder / Xiaoli Xiong / Berend-Jan Bosch / Felix A Rey / David Veesler
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
1.2Nov 8, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Structure viewerMolecule:
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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: Protein/peptide Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 66199.094 Da / Num. of mol.: 3 / Fragment: residues 718-1252 / Source: (gene. exp.) Murine coronavirus / Strain: A59 / Gene: S, 3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P11224
Sequence detailsThe authors state that all the differences between the sequence provided and the sequence database ...The 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 reconstruction

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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 MDa / Experimental value: NO
Source (natural)Organism: Murine hepatitis virus
Source (recombinant)Organism: Drosophila melanogaster (fruit fly)
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 FIELDBright-field microscopy
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
IDNameVersionCategory
2Leginonimage acquisition
4RELION2.0.3CTF correction
7Cootmodel fitting
9RELION2.0.3initial Euler assignment
10RELION2.0.3final Euler assignment
12RELION2.0.33D reconstruction
13Rosettamodel refinement
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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