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- PDB-5x58: Prefusion structure of SARS-CoV spike glycoprotein, conformation 1 -

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Basic information

Entry
Database: PDB / ID: 5x58
TitlePrefusion structure of SARS-CoV spike glycoprotein, conformation 1
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV / spike glycoprotein / prefusion / single particle
Function/homologySpike glycoprotein, N-terminal / Spike glycoprotein N-terminal domain / 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 / receptor-mediated virion attachment to host cell ...Spike glycoprotein, N-terminal / Spike glycoprotein N-terminal domain / 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 / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host endosome membrane / pathogenesis / viral envelope / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding / Spike glycoprotein
Function and homology information
Specimen sourceSARS coronavirus BJ01 / virus
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle) / Transmission electron microscopy
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)419,76845
Polyers410,4783
Non-polymers9,29142
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)44920
ΔGint (kcal/M)1
Surface area (Å2)129290

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Components

#1: Protein/peptide Spike glycoprotein


Mass: 136825.891 Da / Num. of mol.: 3 / Source: (gene. exp.) SARS coronavirus BJ01 / virus / Strain: BJ01 / Production host: Spodoptera frugiperda / References: UniProt:P59594*PLUS
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 42 / Formula: C8H15NO6 / : N-Acetylglucosamine
Sequence detailsTHE REFERENCE SEQUENCE DATABASE OF THIS PROTEIN IS RESIDUES 14-1193 IN GENBANK AAP30030.1. RESIDUES ...THE REFERENCE SEQUENCE DATABASE OF THIS PROTEIN IS RESIDUES 14-1193 IN GENBANK AAP30030.1. RESIDUES 1194-1241 ARE EXPRESSION TAGS.

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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 trimer / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: SARS coronavirus BJ01 / Strain: BJ01
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 FIELD
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range
12AJFE1323-502
25X4SA118-278
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00725942
ELECTRON MICROSCOPYf_angle_d1.12435373
ELECTRON MICROSCOPYf_dihedral_angle_d10.40520831
ELECTRON MICROSCOPYf_chiral_restr0.0654094
ELECTRON MICROSCOPYf_plane_restr0.0064539

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