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- PDB-7p5g: NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506... -

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Basic information

Entry
Database: PDB / ID: 7p5g
TitleNMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O
ComponentsSpike glycoprotein
KeywordsANTIVIRAL PROTEIN / SARS-CoV-2 / mimicking peptides / Spike / Receptor Binding Domain / Covid-19
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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 / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSantoro, A. / Buonocore, M. / Grimaldi, M. / D'Ursi, A.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Heliyon / Year: 2022
Title: Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.
Authors: Buonocore, M. / Santoro, A. / Grimaldi, M. / Covelli, V. / Firoznezhad, M. / Rodriquez, M. / Santin, M. / D'Ursi, A.M.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 5, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Source and taxonomy / Structure summary
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_contact_author / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_validate_torsion / struct_conf
Item: _pdbx_entity_src_syn.organism_common_name / _pdbx_nmr_ensemble.conformers_calculated_total_number ..._pdbx_entity_src_syn.organism_common_name / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_ensemble.conformers_submitted_total_number / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_sample_details.label
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Dec 7, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 2.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)2,7731
Polymers2,7731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3050 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)38 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 2772.996 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 2.5 mM SMIMIC-OR, 50 % v/v Hexafluoroisopropanol, 40 % v/v H2O, 10 % v/v [U-100% 2H] D2O, 50% hexafluoroisopropanol/40% H2O/10% D2O
Label: SMIMIC / Solvent system: 50% hexafluoroisopropanol/40% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMSMIMIC-ORnatural abundance1
50 % v/vHexafluoroisopropanolnatural abundance1
40 % v/vH2Onatural abundance1
10 % v/vD2O[U-100% 2H]1
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 2.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYLeechemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOS-NBaxrefinement
NMRFAM-SPARKYLeepeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 38

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