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

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Basic information

Entry
Database: PDB / ID: 6ack
TitleTrypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 3
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/HYDROLASE / SARS-CoV / spike / glycoprotein / Class I fusion protein / membrane fusion / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex
Function / homologyCoronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Peptidase M2, peptidyl-dipeptidase A / Coronovirus spike glycoprotein, heptad repeat 2 domain / Collectrin domain / Spike glycoprotein, N-terminal / Spike receptor binding domain / Angiotensin-converting enzyme / Coronavirus S2 glycoprotein / Spike receptor binding domain ...Coronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Peptidase M2, peptidyl-dipeptidase A / Coronovirus spike glycoprotein, heptad repeat 2 domain / Collectrin domain / Spike glycoprotein, N-terminal / Spike receptor binding domain / Angiotensin-converting enzyme / Coronavirus S2 glycoprotein / Spike receptor binding domain / Spike receptor binding domain superfamily / Renal amino acid transporter / Neutral zinc metallopeptidases, zinc-binding region signature. / Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / tryptophan transport / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / angiotensin-mediated drinking behavior / receptor biosynthetic process / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of blood vessel diameter / exopeptidase activity / regulation of vasoconstriction / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / carboxypeptidase activity / angiotensin maturation / receptor-mediated virion attachment to host cell / brush border membrane / regulation of cardiac conduction / regulation of cytokine production / metallocarboxypeptidase activity / host cell surface receptor binding / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of inflammatory response / regulation of cell population proliferation / fusion of virus membrane with host endosome membrane / viral entry into host cell / endopeptidase activity / viral envelope / pathogenesis / membrane raft / host cell plasma membrane / virion membrane / cell surface / zinc ion binding / extracellular space / extracellular exosome / integral component of membrane / extracellular region / identical protein binding / plasma membrane / cytoplasm / Spike glycoprotein / Angiotensin-converting enzyme 2
Function and homology information
Specimen sourceHuman SARS coronavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 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
D: Angiotensin-converting enzyme 2


Theoretical massNumber of molelcules
Total (without water)471,2734
Polyers471,2734
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)28600
ΔGint (kcal/M)-140
Surface area (Å2)157730

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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
#2: Protein/peptide Angiotensin-converting enzyme 2 / / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69982.562 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885Angiotensin-converting enzyme 2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2

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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

Component
IDNameTypeEntity IDParent IDSource
1Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complexCOMPLEX1, 20RECOMBINANT
2Trypsin-cleaved and low pH-treated SARS-CoV spikeCOMPLEX11RECOMBINANT
3human ACE2COMPLEX21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12227859SARS coronavirus
239606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
127108Spodoptera frugiperda (fall armyworm)
237108Spodoptera 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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 / Electron dose: 50 / 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: 4.5 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 56553 / Symmetry type: POINT

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