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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 / homologyCoronavirus S2 glycoprotein / 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 / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell ...Coronavirus S2 glycoprotein / 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 / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding / Spike glycoprotein
Function and homology information
Specimen sourceSARS coronavirus BJ01
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 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
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 / Strain: BJ01 / Production host: Spodoptera frugiperda (fall armyworm) / 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 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 8 / 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 / 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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