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- PDB-7k3g: SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Stru... -

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Basic information

Entry
Database: PDB / ID: 7k3g
TitleSARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR
ComponentsEnvelope small membrane protein
KeywordsVIRAL PROTEIN / Viroporin / Pentameric Ion Channel / Transmembrane Domain
Function / homology
Function and homology information


disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / Regulation of gap junction activity / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment / Maturation of protein E / monoatomic ion channel activity ...disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / Regulation of gap junction activity / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment / Maturation of protein E / monoatomic ion channel activity / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / identical protein binding / membrane
Similarity search - Function
Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile.
Similarity search - Domain/homology
Envelope small membrane protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLID-STATE NMR / simulated annealing
AuthorsMandala, V.S. / Hong, M. / McKay, M.J. / Shcherbakov, A.S. / Dregni, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088204 United States
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers.
Authors: Mandala, V.S. / McKay, M.J. / Shcherbakov, A.A. / Dregni, A.J. / Kolocouris, A. / Hong, M.
#1: Journal: Res Sq / Year: 2020
Title: Structure and Drug Binding of the SARS-CoV-2 Envelope Protein in Phospholipid Bilayers.
Authors: Hong, M. / Mandala, V. / McKay, M. / Shcherbakov, A. / Dregni, A. / Kolocouris, A.
History
DepositionSep 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 21, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nmr_representative ...atom_site / pdbx_nmr_representative / pdbx_validate_torsion / struct_conf
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _pdbx_nmr_representative.selection_criteria / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Description: Polymer geometry
Details: We have recalculated the slightly structures to obtain better agreement with known sidechain rotamers. The structural ensemble is overall very similar to before.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Nov 25, 2020Group: Database references / Category: citation / citation_author
Revision 2.3Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.5May 15, 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: Envelope small membrane protein
B: Envelope small membrane protein
C: Envelope small membrane protein
D: Envelope small membrane protein
E: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)16,8115
Polymers16,8115
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: literature evidence using analytical ultracentrifugation and gel electrophoresis indicate pentamers are the most likely oligomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6330 Å2
ΔGint-77 kcal/mol
Surface area9660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 192structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide
Envelope small membrane protein / sM protein


Mass: 3362.115 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: E, 4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DTC4

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D CC CORD
121anisotropic12D NCA/NCO SPEC-CP
131anisotropic13D NCACX/NCOCX/CONCA
142anisotropic31D/2D 13C-19F REDOR
152anisotropic32D 13C-19F SPEC-CP
163anisotropic22D NHHC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
membrane10.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous bufferU-13C15N, ERGICaqueous buffer
membrane20.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [4-19F-Phe] fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer1:1 19F-Phe:U-13C15N, ERGICaqueous buffer
membrane30.1 mg/uL [U-15N] 15N SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [U-13C] 13C SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer1:1 U-15N:U-13C, ERGICaqueous buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mg/uLSARS-CoV-2 Envelope Protein Transmembrane Domain[U-13C; U-15N]1
0.23 mg/uLPOPCnatural abundance1
0.1 mg/uLPOPEnatural abundance1
0.08 mg/uLbovine PInatural abundance1
0.04 mg/uLPOPSnatural abundance1
0.04 mg/uLCholesterolnatural abundance1
0.1 mg/uLSARS-CoV-2 Envelope Protein Transmembrane Domain[U-13C; U-15N]2
0.1 mg/uLfluoro SARS-CoV-2 Envelope Protein Transmembrane Domain[4-19F-Phe]2
0.23 mg/uLPOPCnatural abundance2
0.1 mg/uLPOPEnatural abundance2
0.08 mg/uLbovine PInatural abundance2
0.04 mg/uLPOPSnatural abundance2
0.04 mg/uLCholesterolnatural abundance2
0.1 mg/uL15N SARS-CoV-2 Envelope Protein Transmembrane Domain[U-15N]3
0.1 mg/uL13C SARS-CoV-2 Envelope Protein Transmembrane Domain[U-13C]3
0.23 mg/uLPOPCnatural abundance3
0.1 mg/uLPOPEnatural abundance3
0.08 mg/uLbovine PInatural abundance3
0.04 mg/uLPOPSnatural abundance3
0.04 mg/uLCholesterolnatural abundance3
Sample conditionsIonic strength: 20 mM / Label: pH75_ERGIC / pH: 7.5 / PH err: 0.2 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO9001
Bruker AVANCE IIBrukerAVANCE II8002
Bruker AVANCE III HDBrukerAVANCE III HD603

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKYNMRFAMchemical shift assignment
TopSpinBruker Biospinprocessing
X-PLOR NIH2.47Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH2.47Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 192 / Conformers submitted total number: 10

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