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- PDB-8u1t: SARS-CoV-2 Envelope Protein Transmembrane Domain: Dimeric Structu... -

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Basic information

Entry
Database: PDB / ID: 8u1t
TitleSARS-CoV-2 Envelope Protein Transmembrane Domain: Dimeric Structure Determined by Solid-State NMR
ComponentsEnvelope small membrane protein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Envelope protein / E protein / Transmembrane domain / Membrane protein / PISEMA / PISA wheel / DARR
Function / homology
Function and homology information


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 ...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 / membrane / identical protein binding
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
AuthorsZhang, R. / Qin, H. / Prasad, R. / Fu, R. / Zhou, H.X. / Cross, T.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119187 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122698 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118091 United States
National Science Foundation (NSF, United States)DMR1644779 United States
National Science Foundation (NSF, United States)DMR2128556 United States
Citation
Journal: Commun Biol / Year: 2023
Title: Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.
Authors: Zhang, R. / Qin, H. / Prasad, R. / Fu, R. / Zhou, H.X. / Cross, T.A.
#1: Journal: Biorxiv / Year: 2023
Title: Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.
Authors: Zhang, R. / Qin, H. / Prasad, R. / Fu, R. / Zhou, H.X. / Cross, T.A.
History
DepositionSep 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 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

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Assembly

Deposited unit
A: Envelope small membrane protein
B: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)6,1782
Polymers6,1782
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3088.807 Da / Num. of mol.: 2
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) / 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
111anisotropic22D 1H-15N PISEMA
122anisotropic22D 1H-15N PISEMA
133anisotropic22D 1H-15N PISEMA
144anisotropic22D 1H-15N PISEMA
155anisotropic22D 1H-15N PISEMA
166anisotropic22D 1H-15N PISEMA
177anisotropic22D 1H-15N PISEMA
188anisotropic12D 1H-13C DARR
1910anisotropic12D 1H-13C DARR
1109anisotropic12D 1H-13C DARR
21111anisotropic21D zg

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
liposome180 ug/mL [U-100% 15N] SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N_ETMAqueous buffer
liposome280 ug/mL [U-15N]-Ile SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N-Ile_ETMAqueous buffer
liposome380 ug/mL [U-15N]-Phe SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N-Phe_ETMAqueous buffer
liposome480 ug/mL [U-15N]-Ala SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N-Ala_ETMAqueous buffer
liposome580 ug/mL [U-15N]-Val SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N-Val_ETMAqueous buffer
liposome680 ug/mL [U-15N]-Thr SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N-Thr_ETMAqueous buffer
liposome780 ug/mL [U-15N]-Leu SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer15N-Leu_ETMAqueous buffer
liposome840 ug/mL [U-13C]-Leu, [U-13C]-Val SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer13C-Leu_13C-Val_ETMAqueous buffer
liposome920 ug/mL [U-13C]-Leu, [U-13C]-Phe SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer13C-Leu_13C-Phe_ETMAqueous buffer
liposome1020 ug/mL [U-13C]-Val, [U-13C]-Met SARS-CoV-2 envelope protein transmembrane peptide, 400 ug/mL POPC, 100 ug/mL POPG, Aqueous buffer13C-Val_13C-Met_ETMAqueous buffer
liposome11100 saturated [U-15N] ammonium chloride salt, Aqueous buffer15NH4ClAqueous buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-100% 15N]1
400 ug/mLPOPCnatural abundance1
100 ug/mLPOPGnatural abundance1
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-15N]-Ile2
400 ug/mLPOPCnatural abundance2
100 ug/mLPOPGnatural abundance2
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-15N]-Phe3
400 ug/mLPOPCnatural abundance3
100 ug/mLPOPGnatural abundance3
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-15N]-Ala4
400 ug/mLPOPCnatural abundance4
100 ug/mLPOPGnatural abundance4
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-15N]-Val5
400 ug/mLPOPCnatural abundance5
100 ug/mLPOPGnatural abundance5
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-15N]-Thr6
400 ug/mLPOPCnatural abundance6
100 ug/mLPOPGnatural abundance6
80 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-15N]-Leu7
400 ug/mLPOPCnatural abundance7
100 ug/mLPOPGnatural abundance7
40 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-13C]-Leu, [U-13C]-Val8
400 ug/mLPOPCnatural abundance8
100 ug/mLPOPGnatural abundance8
20 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-13C]-Leu, [U-13C]-Phe9
400 ug/mLPOPCnatural abundance9
100 ug/mLPOPGnatural abundance9
20 ug/mLSARS-CoV-2 envelope protein transmembrane peptide[U-13C]-Val, [U-13C]-Met10
400 ug/mLPOPCnatural abundance10
100 ug/mLPOPGnatural abundance10
100 saturatedammonium chloride salt[U-15N]11
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
15 mM17.5 1 atm295 K
25 Not defined17.5 Not defined1 atm295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospindata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NAMDUniversity of Illinois at Urbana Champaign: Theoretical and Computational Biophysics Group (TCB), Parallel Programming Laboratory (PPL)refinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 14

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