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- PDB-6acd: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein an... -

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Basic information

Entry
Database: PDB / ID: 6acd
TitleTrypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-free conformation with one RBD in up conformation
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV / spike / glycoprotein / Class I fusion protein / membrane fusion
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 sourceHuman SARS coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsGui, M. / Song, W.
CitationJournal: PLoS Pathog. / Year: 2018
Title: Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2.
Authors: Wenfei Song / Miao Gui / Xinquan Wang / Ye Xiang
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2018 / Release: Aug 8, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 8, 2018Structure modelrepositoryInitial release
1.1Aug 22, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)401,2903
Polyers401,2903
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)28740
ΔGint (kcal/M)-134
Surface area (Å2)137720

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Components

#1: Protein/peptide Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 133763.422 Da / Num. of mol.: 3 / Source: (gene. exp.) Human SARS coronavirus / Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594

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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: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: SARS coronavirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 5.8
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 FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 174489 / Symmetry type: POINT

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