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- PDB-5xer: TK9 NMR structure in DPC micelle -

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Basic information

Entry
Database: PDB / ID: 5xer
TitleTK9 NMR structure in DPC micelle
ComponentsTHR-VAL-TYR-VAL-TYR-SER-ARG-VAL-LYS
KeywordsPROTEIN FIBRIL / CYANA 2.1
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 speciesSARS coronavirus
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsGhosh, A. / Bhunia, A.
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2018
Title: Structural insights of a self-assembling 9-residue peptide from the C-terminal tail of the SARS corona virus E-protein in DPC and SDS micelles: A combined high and low resolution spectroscopic study.
Authors: Ghosh, A. / Bhattacharyya, D. / Bhunia, A.
History
DepositionApr 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: THR-VAL-TYR-VAL-TYR-SER-ARG-VAL-LYS


Theoretical massNumber of molelcules
Total (without water)1,1161
Polymers1,1161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1160 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide THR-VAL-TYR-VAL-TYR-SER-ARG-VAL-LYS


Mass: 1116.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SARS coronavirus / References: UniProt: P59637*PLUS

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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

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Sample preparation

DetailsType: solution
Contents: 1.0 mM TK9, 55.55 M H2O, 125 mM [U-100% 2H] DPC, 90% H2O/10% D2O
Label: TK9 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMTK9natural abundance1
55.55 MH2Onatural abundance1
125 mMDPC[U-100% 2H]1
Sample conditionsIonic strength: 125 mM mM / Label: conditions_1 / pH: 4.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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