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- PDB-6nzk: Structural basis for human coronavirus attachment to sialic acid ... -

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Entry
Database: PDB / ID: 6nzk
TitleStructural basis for human coronavirus attachment to sialic acid receptors
ComponentsSpike surface glycoprotein
KeywordsVIRAL PROTEIN / Coronavirus spike glycoprotein / sialic acid / HCoV-OC43 / fusion protein
Function / homology
Function and homology information


membrane fusion / receptor-mediated virion attachment to host cell / viral envelope / integral component of membrane
Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / Coronavirus S2 glycoprotein / Spike receptor binding domain / Spike glycoprotein N-terminal domain
Spike surface glycoprotein
Biological speciesHuman coronavirus OC43
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTortorici, M.A. / Walls, A.C. / Lang, Y. / Wang, C. / Li, Z. / Koerhuis, D. / Boons, G.J. / Bosch, B.J. / Rey, F.A. / de Groot, R. / Veesler, D.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM120553United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Structural basis for human coronavirus attachment to sialic acid receptors.
Authors: M Alejandra Tortorici / Alexandra C Walls / Yifei Lang / Chunyan Wang / Zeshi Li / Danielle Koerhuis / Geert-Jan Boons / Berend-Jan Bosch / Félix A Rey / Raoul J de Groot / David Veesler /
Abstract: Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host ...Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host receptors and fuses the viral and cellular membranes. To understand the molecular basis of coronavirus attachment to oligosaccharide receptors, we determined cryo-EM structures of coronavirus OC43 S glycoprotein trimer in isolation and in complex with a 9-O-acetylated sialic acid. We show that the ligand binds with fast kinetics to a surface-exposed groove and that interactions at the identified site are essential for S-mediated viral entry into host cells, but free monosaccharide does not trigger fusogenic conformational changes. The receptor-interacting site is conserved in all coronavirus S glycoproteins that engage 9-O-acetyl-sialogycans, with an architecture similar to those of the ligand-binding pockets of coronavirus hemagglutinin esterases and influenza virus C/D hemagglutinin-esterase fusion glycoproteins. Our results demonstrate these viruses evolved similar strategies to engage sialoglycans at the surface of target cells.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 13, 2019 / Release: Jun 5, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 5, 2019Structure modelrepositoryInitial release
1.1Jun 19, 2019Structure modelData collection / Data processing / Database referencescitation / citation_author / em_3d_reconstruction_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_3d_reconstruction.resolution

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)461,866108
Polymers439,3153
Non-polymers22,551105
Water7,134396
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53240 Å2
ΔGint139 kcal/mol
Surface area150800 Å2

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Components

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Protein/peptide , 1 types, 3 molecules ABC

#1: Protein/peptide Spike surface glycoprotein


Mass: 146438.312 Da / Num. of mol.: 3 / Mutation: R754G,R755G,R757G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus OC43 / Production host: Homo sapiens (human) / References: UniProt: Q696P8

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Non-polymers , 5 types, 501 molecules

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


Mass: 221.208 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical...
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#4: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#5: Chemical ChemComp-MJJ / methyl 9-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid


Mass: 365.333 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C14H23NO10
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O / Water

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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: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Betacoronavirus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-1.2/1.3 4C
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: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginon3.3image acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178356 / Symmetry type: POINT

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