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- PDB-7my8: Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Insert... -

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Basic information

Entry
Database: PDB / ID: 7my8
TitleFusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles
ComponentsSpike protein S2
KeywordsLIPID BINDING PROTEIN / Fusion Peptide
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / molecular dynamics
AuthorsKoppisetti, R.K. / Fulcher, Y.G. / Van Doren, S.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2030473 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles.
Authors: Koppisetti, R.K. / Fulcher, Y.G. / Van Doren, S.R.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 8, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S2


Theoretical massNumber of molelcules
Total (without water)4,5851
Polymers4,5851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Spike protein S2 / Spike Fusion Peptide


Mass: 4585.220 Da / Num. of mol.: 1 / Fragment: residues 816-857
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia phage Ecwhy_1 (virus) / References: UniProt: P0DTC2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY
122isotropic22D 1H-13C HSQC aliphatic
132isotropic23D HNCO
142isotropic23D HN(CA)CO
152isotropic23D CBCA(CO)NH
162isotropic23D HN(CA)CB
172isotropic23D C(CO)NH
182isotropic23D H(CCO)NH
192isotropic23D (H)CCH-TOCSY
1102isotropic23D 15N Separated NOESY
1112isotropic23D 13C Separated NOESY
1122isotropic23D 13C TROSY edited NOESY
1132isotropic22D 13C (Hb)Cb(CgCd)Hd
1142isotropic22D 13C (Hb)Cb(CgCd)He

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-99% 15N] Spike Fusion Peptide, Bicelles, 90% H2O/10% D2O15N90% H2O/10% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] Spike Fusion Peptide, Bicelles, 90% H2O/10% D2O13C,15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMSpike Fusion Peptide, Bicelles[U-99% 15N]1
0.4 mMSpike Fusion Peptide, Bicelles[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 0 M / Label: 20mm Tris-Acetate / pH: 5 / Pressure: 0 Pa / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKYWoonghee Lee , Marco Tonelli , John L Markleychemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
GROMACSBerendsenrefinement
NMRFAM-SPARKYWoonghee Lee , Marco Tonelli , John L Markleypeak picking
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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