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

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Entry
Database: PDB / ID: 5x59
TitlePrefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry
DescriptorS protein
KeywordsVIRAL PROTEIN / MERS-CoV / spike glycoprotein / prefusion / single particle
Specimen sourceMiddle East respiratory syndrome coronavirus / virus
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle)
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.
CitationNat Commun, 2017, 8, 15092-15092

Nat Commun, 2017, 8, 15092-15092 StrPapers
Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
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
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: Polypeptide(L)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
References: UniProt: W6A028

Cellular component

Biological process

#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


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

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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: 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 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: 3.7 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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