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- PDB-3jcl: Cryo-electron microscopy structure of a coronavirus spike glycopr... -

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Basic information

Entry
Database: PDB / ID: 3jcl
TitleCryo-electron microscopy structure of a coronavirus spike glycoprotein trimer
ComponentsSpike glycoproteinSpike protein
KeywordsVIRAL PROTEIN / Coronavirus / viral fusion proteins / viral spike / peplomer
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / 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 / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike glycoprotein, N-terminal domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike glycoprotein, N-terminal domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine hepatitis virus strain A59
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsWalls, A.C. / Tortorici, M.A. / Bosch, B.J. / Frenz, B. / Rottier, P.J.M. / DiMaio, F. / Rey, F.A. / Veesler, D.
CitationJournal: Nature / Year: 2016
Title: Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer.
Authors: Alexandra C Walls / M Alejandra Tortorici / Berend-Jan Bosch / Brandon Frenz / Peter J M Rottier / Frank DiMaio / Félix A Rey / David Veesler /
Abstract: The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the ...The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a mouse coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)419,1873
Polymers419,1873
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein / Spike protein S1 / 90B / Spike protein S2 / 90A


Mass: 139728.984 Da / Num. of mol.: 3 / Fragment: UNP residues 15-1231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine hepatitis virus strain A59 / Strain: A59 / Gene: 3, S / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P11224

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Murine hepatitis virus protein S / Type: VIRUS / Details: Trimer
Molecular weightValue: 0.42 MDa / Experimental value: NO
Buffer solutionName: 20 mM Tris-HCl, 100 mM NaCl / pH: 7.5 / Details: 20 mM Tris-HCl, 100 mM NaCl
SpecimenConc.: 1.85 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 93 K / Humidity: 90 %
Details: Blot for 3.5 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
Method: Blot for 3.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 9, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 38022 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 1600

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2Rosettamodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionMethod: Projection-matching / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82000 / Nominal pixel size: 1.46 Å / Actual pixel size: 1.46 Å / Details: (Single particle--Applied symmetry: C3) / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--flexible
Atomic model building
IDPDB-ID 3D fitting-ID
14KQZ

4kqz

1
24H14

4h14

1
33R4D

3r4d

1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms24822 0 0 0 24822

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