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- PDB-5x29: NMR structure of the SARS Coronavirus E protein pentameric ion channel -

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Basic information

Entry
Database: PDB / ID: 5x29
TitleNMR structure of the SARS Coronavirus E protein pentameric ion channel
ComponentsEnvelope small membrane protein
KeywordsVIRAL PROTEIN / membrane protein / envelope protein / ion channel / pentamer
Function / homology
Function and homology information


SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / disruption of plasma membrane integrity in another organism / Translation of Structural Proteins / Virion Assembly and Release / SARS-CoV-1-mediated effects on programmed cell death / host cell Golgi membrane / Attachment and Entry / Maturation of protein E / SARS-CoV-1 activates/modulates innate immune responses ...SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / disruption of plasma membrane integrity in another organism / Translation of Structural Proteins / Virion Assembly and Release / SARS-CoV-1-mediated effects on programmed cell death / host cell Golgi membrane / Attachment and Entry / Maturation of protein E / SARS-CoV-1 activates/modulates innate immune responses / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / 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 speciesHuman SARS coronavirus
MethodSOLUTION NMR / simulated annealing
AuthorsTorres, J. / Surya, W. / Li, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of EducationRG 51/13 Singapore
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Structural model of the SARS coronavirus E channel in LMPG micelles
Authors: Surya, W. / Li, Y. / Torres, J.
History
DepositionJan 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 4, 2018Group: Data collection / Database references / Polymer sequence
Category: citation / citation_author / entity_poly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_poly.pdbx_target_identifier
Revision 2.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.2May 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:
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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)45,0185
Polymers45,0185
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6250 Å2
ΔGint-57 kcal/mol
Surface area22590 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein
Envelope small membrane protein / sM protein


Mass: 9003.540 Da / Num. of mol.: 5 / Fragment: UNP residues 8-65 / Mutation: C40A, C43A, C44A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: E, sM, 4 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P59637

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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 HSQC
122isotropic13D HNCA
132isotropic13D HN(CO)CA
142isotropic13D (H)CCH-TOCSY
152isotropic13D 1H-15N NOESY
172isotropic12D 1H-13C HSQC
162isotropic13D 1H-13C NOESY
183isotropic13D 1H-15N NOESY
194isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.67 mM [U-99% 15N] Envelope small membrane protein, 200 mM LMPG, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
micelle20.67 mM [U-99% 13C; U-99% 15N] Envelope small membrane protein, 200 mM LMPG, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N13C_sample95% H2O/5% D2O
micelle30.67 mM [U-99% 15N, U-99% 2H] Envelope small membrane protein, 200 mM LMPG, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N2H_sample95% H2O/5% D2O
micelle40.33 mM [U-99% 13C] Envelope small membrane protein, 0.33 mM [U-99% 15N, U-99% 2H] Envelope small membrane protein, 200 mM LMPG, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N2H+13C_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.67 mMEnvelope small membrane protein[U-99% 15N]1
200 mMLMPGnatural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.67 mMEnvelope small membrane protein[U-99% 13C; U-99% 15N]2
200 mMLMPGnatural abundance2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
0.67 mMEnvelope small membrane protein[U-99% 15N, U-99% 2H]3
200 mMLMPGnatural abundance3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
0.33 mMEnvelope small membrane protein[U-99% 15N, U-99% 2H]4
200 mMLMPGnatural abundance4
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
HADDOCK2.2Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: Calculation of pentamer structure
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 16

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