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

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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 / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into 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 / pathogenesis ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into 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 / pathogenesis / integral component of membrane / identical protein binding
Spike glycoprotein N-terminal domain / Spike receptor binding domain superfamily / Spike receptor binding domain / Spike glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal
Spike glycoprotein
Biological speciesSARS coronavirus BJ01
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
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.
Funding support China, 11items
OrganizationGrant numberCountry
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08020100 China
China Ministry of Science and Technology (MOST) National 973 Project2013CB531502 China
China Ministry of Science and Technology (MOST) National 973 Project2014CB542503 China
the National Key Research and Development Program of China2016YFD0500300 China
the China National Grand S&T Special Project2014ZX10004-001-006 China
the Natural Science Foundation of China31570874 China
the Natural Science Foundation of China81461168030 China
the Excellent Young Scientist Program from the NSFC81622031 China
Excellent Young Scientist Program of the Chinese Academy of Sciences and the Youth Innovation Promotion Association CAS2015078 China
National Thousand (Young) Talents Program China
leading principal investigator of the NSFC Innovative Research Group81321063 China
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
History
DepositionFeb 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release

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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
Polymers410,4783
Non-polymers9,29142
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44920 Å2
ΔGint1 kcal/mol
Surface area129290 Å2

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Components

#1: Protein Spike glycoprotein


Mass: 136825.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus BJ01 / Strain: BJ01 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594*PLUS
#2: Sugar...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 42
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 / 3D reconstruction method: single particle reconstruction

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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 (fall armyworm)
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
MicroscopyModel: 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-IDPdb chain-ID3D fitting-IDPdb chain residue range
12AJFE1323-502
25X4SA118-278
Refine LS restraints
Refinement-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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