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- PDB-6lxf: Aromatic interactions drive the coupled folding and binding of th... -

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Basic information

Entry
Database: PDB / ID: 6lxf
TitleAromatic interactions drive the coupled folding and binding of the intrinsically disordered Sesbania mosaic virus VPg protein.
ComponentsPolyprotein
KeywordsPLANT VIRAL PROTEIN / IDPs (Intrinsically Disorder Proteins) / VPg (Viral Protein genome linked)
Function / homology
Function and homology information


host cell membrane / viral translational frameshifting / serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Peptidase S39 / Peptidase S39B, luteovirus / Peptidase family S39 domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesSesbania mosaic virus
MethodSOLUTION NMR / na
AuthorsDixit, K. / Karanth, N.M. / Nair, S. / Kumari, K. / Chakrabarti, K.S. / Savithri, H.S. / Sarma, S.P.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
Department of Biotechnology (DBT, India) India
CitationJournal: Biochemistry / Year: 2020
Title: Aromatic Interactions Drive the Coupled Folding and Binding of the Intrinsically Disordered Sesbania mosaic Virus VPg Protein.
Authors: Dixit, K. / Karanth, N.M. / Nair, S. / Kumari, K. / Chakrabarti, K.S. / Savithri, H.S. / Sarma, S.P.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Jun 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 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
B: Polyprotein


Theoretical massNumber of molelcules
Total (without water)6,5681
Polymers6,5681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 999target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Polyprotein / Viral Protein genome linked (SeMV VPg)


Mass: 6568.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9EB08

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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
121isotropic13D TROSY ENHANCED HNCA
131isotropic13D TROSY ENHANCED HN(CO)CA
141isotropic13D TROSY ENHANCED HN(CA)CB
151isotropic13D TROSY ENHANCED HN(COCA)CB
161isotropic13D HNCO
171isotropic13D 1H-15N NOESY
181isotropic12D 1H-13C HSQC aliphatic
191isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-13C; U-15N; U-2H] SELECTIVELY 1H (CH3) ILE, VAL, LEU Sesbania Mosaic Virus- Viral Protein genome linked (SeMV VPg), 90% H2O/10% D2O
Details: 0.3 mM [U-13C; U-15N; U-2H] SELECTIVELY 1H (CH3) ILE, VAL, LEU VIRAL PROTEIN GENOME LINKED (VPG) FROM SESBANIA MOSAIC VIRUS
Label: U-13C, 15N, 2H selectively 1H (CH3) ILV / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM
Component: Sesbania Mosaic Virus- Viral Protein genome linked (SeMV VPg)
Isotopic labeling: [U-13C; U-15N; U-2H] SELECTIVELY 1H (CH3) ILE, VAL, LEU
Sample conditionsIonic strength: 0.065 Not defined / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Uniform NMR System / Manufacturer: Agilent / Model: Uniform NMR System / Field strength: 600 MHz
Details: Agilent (Varian) DDS2 600 MHz spectrometer equipped with a cryogenically cooled cold-probe fitted with a pulsed field gradient (z-axis only) accessory

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.1-2.4CCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 999 / Conformers submitted total number: 25

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