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- PDB-8suz: Open State of the SARS-CoV-2 Envelope Protein Transmembrane Domai... -

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Open data


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Basic information

Entry
Database: PDB / ID: 8suz
TitleOpen State of the SARS-CoV-2 Envelope Protein Transmembrane Domain, Determined by Solid-State NMR
ComponentsEnvelope small membrane protein
KeywordsVIRAL PROTEIN / Viroporin / SARS-CoV-2 / Cation Channel
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
AuthorsMedeiros-Silva, J. / Dregni, A.J. / Somberg, N.H. / Hong, M.
Funding support United States, Netherlands, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM088204 United States
Netherlands Organisation for Scientific Research (NWO)452020132 Netherlands
CitationJournal: Sci Adv / Year: 2023
Title: Atomic structure of the open SARS-CoV-2 E viroporin.
Authors: Medeiros-Silva, J. / Dregni, A.J. / Somberg, N.H. / Duan, P. / Hong, M.
History
DepositionMay 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / 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: 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: native gel electrophoresis, NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3920 Å2
ΔGint-41 kcal/mol
Surface area11950 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1medoid

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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 / Variant: Wuhan-Hu-1 / Plasmid: Champion pET-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
111isotropic22D 15N-13C
121isotropic22D 13C-detected CORD
131isotropic22D 1H-15N CP HETCOR
242isotropic12D 15N-13C PSD
151isotropic23D HNCA
161isotropic33D HN(CO)CA
173isotropic31D 19F 13C-detected REDOR
184isotropic32D 19F 1H-15N 1H-detected CP HETCOR
395isotropic23D NCa-filtered 13C-detected DIPSHIFT

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
liposome115.5 % w/w [U-99% 13C; U-99% 15N] ETM, 23 % w/w POPC, 3.5 % w/w POPS, 10 % w/w POPE, 8 % w/w PI, 4 % w/w Cholesterol, 36 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2OETM reconstituted in liposomes based on the lipid composition of the ER-Golgi Intermediate Compartment, reconstituted in acidic pH and calcium[13C/15N] ETM ERGIC95% H2O/5% D2O
liposome27.5 % w/w [U-99% 15N; U-80% 2H] ETM, 8 % w/w [U-100% 13C] ETM, 23 % w/w POPC, 3.5 % w/w POPS, 10 % w/w POPE, 8 % w/w PI, 4 % w/w Cholesterol, 36 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2OETM reconstituted in liposomes based on the lipid composition of the ER-Golgi Intermediate Compartment, reconstituted in acidic pH and calcium[13C]+[15N] Mix ETM ERGIC95% H2O/5% D2O
liposome37.5 % w/w [U-100% 13C; U-100% 15N; U-80% 2H] ETM, 8 % w/w 4-19F-Phe20-ETM, 23 % w/w POPC, 11 % w/w POPS, 10 % w/w POPE, 4.5 % w/w Cholesterol, 36 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2OETM reconstituted in liposomes based on the lipid composition of the ER-Golgi Intermediate Compartment, reconstituted in acidic pH and calcium. PI lipids were excluded[13C]+[19F-Phe20] Mix ETM ERGIC95% H2O/5% D2O
liposome44.5 % w/w [U-99% 13C; U-99% 15N] ETM, 4 % w/w 4-19F-Phe20-ETM, 36.5 % w/w DMPC, 16 % w/w DMPG, 39 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2OETM reconstituted in DMPC/DMPG liposomes, reconstituted in acidic pH and calcium[13C/5N/(2H/1H)]+[19F-Phe20] Mix ETM DMPX95% H2O/5% D2O
liposome58.5 % w/w [U-99% 13C; U-99% 15N] ETM, 35 % w/w POPC, 15.5 % w/w POPG, 59 % w/w Water, 30 mM sodium acetate, 30 mM calcium chloride, 10 mM sodium chloride, 95% H2O/5% D2OETM reconstituted in liposomes POPC/POPG, reconstituted in acidic pH and calcium[13C/15N] ETM POPX95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15.5 % w/wETM[U-99% 13C; U-99% 15N]1
23 % w/wPOPCnatural abundance1
3.5 % w/wPOPSnatural abundance1
10 % w/wPOPEnatural abundance1
8 % w/wPInatural abundance1
4 % w/wCholesterolnatural abundance1
36 % w/wWaternatural abundance1
30 mMsodium acetatenatural abundance1
30 mMcalcium chloridenatural abundance1
10 mMsodium chloridenatural abundance1
7.5 % w/wETM[U-99% 15N; U-80% 2H]2
8 % w/wETM domain[U-100% 13C]2
23 % w/wPOPCnatural abundance2
3.5 % w/wPOPSnatural abundance2
10 % w/wPOPEnatural abundance2
8 % w/wPInatural abundance2
4 % w/wCholesterolnatural abundance2
36 % w/wWaternatural abundance2
30 mMsodium acetatenatural abundance2
30 mMcalcium chloridenatural abundance2
10 mMsodium chloridenatural abundance2
7.5 % w/wETM[U-100% 13C; U-100% 15N; U-80% 2H]3
8 % w/w4-19F-Phe20-ETMnatural abundance3
23 % w/wPOPCnatural abundance3
11 % w/wPOPSnatural abundance3
10 % w/wPOPEnatural abundance3
4.5 % w/wCholesterolnatural abundance3
36 % w/wWaternatural abundance3
30 mMsodium acetatenatural abundance3
30 mMcalcium chloridenatural abundance3
10 mMsodium chloridenatural abundance3
4.5 % w/wETM[U-99% 13C; U-99% 15N]4
4 % w/w4-19F-Phe20-ETMnatural abundance4
36.5 % w/wDMPCnatural abundance4
16 % w/wDMPGnatural abundance4
39 % w/wWaternatural abundance4
30 mMsodium acetatenatural abundance4
30 mMcalcium chloridenatural abundance4
10 mMsodium chloridenatural abundance4
8.5 % w/wETM[U-99% 13C; U-99% 15N]5
35 % w/wPOPCnatural abundance5
15.5 % w/wPOPGnatural abundance5
59 % w/wWaternatural abundance5
30 mMsodium acetatenatural abundance5
30 mMcalcium chloridenatural abundance5
10 mMsodium chloridenatural abundance5
Sample conditions

Details: Sample Under Magic Angle Spinning / Ionic strength: 1 M / pH: 4.5 / Pressure: 1 atm / Temperature err: 2

Conditions-IDLabelTemperature (K)
11283 K
22273 K
35331 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE NEOBrukerAVANCE NEO6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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