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- PDB-5x59: Prefusion structure of MERS-CoV spike glycoprotein, three-fold sy... -

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Basic information

Entry
Database: PDB / ID: 5x59
TitlePrefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry
ComponentsS protein
KeywordsVIRAL PROTEIN / MERS-CoV / spike glycoprotein / prefusion / single particle
Function / homologyhost cell endoplasmic reticulum-Golgi intermediate compartment membrane / Spike receptor binding domain / Spike receptor binding domain superfamily / Coronovirus spike glycoprotein, heptad repeat 2 domain / Coronavirus S2 glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain / membrane fusion / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Spike receptor binding domain / Spike receptor binding domain superfamily / Coronovirus spike glycoprotein, heptad repeat 2 domain / Coronavirus S2 glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain / membrane fusion / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / pathogenesis / virion membrane / integral component of membrane / Spike glycoprotein / S protein
Function and homology information
Specimen sourceMiddle East respiratory syndrome coronavirus / / virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsYuan, Y. / Cao, D. / Zhang, Y. / Ma, J. / Qi, J. / Wang, Q. / Lu, G. / Wu, Y. / Yan, J. / Shi, Y. / Zhang, X. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2017
Title: Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Authors: Yuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao
Abstract: The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and ...The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2017 / Release: May 3, 2017
RevisionDateData content typeGroupProviderType
1.0May 3, 2017Structure modelrepositoryInitial release
1.1May 24, 2017Structure modelRefinement description

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)444,20533
Polyers437,5693
Non-polymers6,63630
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)31230
ΔGint (kcal/M)-26
Surface area (Å2)145540

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Components

#1: Protein/peptide S protein / Spike glycoprotein / Spike protein


Mass: 145856.203 Da / Num. of mol.: 3 / Fragment: UNP residues 18-1294 / Mutation: R751S, R1020Q
Source: (gene. exp.) Middle East respiratory syndrome coronavirus / / virus
Production host: Spodoptera frugiperda / References: UniProt:W6A028, UniProt:K9N5Q8*PLUS
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 30 / Formula: C8H15NO6 / N-Acetylglucosamine

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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: MERS-CoV spike trimer / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Middle East respiratory syndrome coronavirus
Source (recombinant)Organism: Spodoptera frugiperda
Buffer solutionpH: 7.5
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 FIELDBright-field microscopy
Image recordingElectron dose: 8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2411: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01313968
ELECTRON MICROSCOPYf_angle_d1.96218954
ELECTRON MICROSCOPYf_dihedral_angle_d10.61611382
ELECTRON MICROSCOPYf_chiral_restr0.0912160
ELECTRON MICROSCOPYf_plane_restr0.0112457

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