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- PDB-6nfw: Potyvirus viral protein genome linked (VPg) emulates the m7G cap ... -

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Basic information

Entry
Database: PDB / ID: 6nfw
TitlePotyvirus viral protein genome linked (VPg) emulates the m7G cap to recruit the eukaryotic translation initiation factor eIF4E
ComponentsVPg
KeywordsVIRAL PROTEIN / Potyvirus
Function / homologyPotyvirus NIa protease (NIa-pro) domain / Peptidase family C4 / Potyvirus NIa protease (NIa-pro) domain profile. / cysteine-type peptidase activity / membrane => GO:0016020 / Peptidase S1, PA clan, chymotrypsin-like fold / Polyprotein / VPg
Function and homology information
Biological speciesPotato virus Y
MethodSOLUTION NMR / simulated annealing
AuthorsBorden, K. / Volpon, L. / Osborne, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural studies of the eIF4E-VPg complex reveal a direct competition for capped RNA: Implications for translation.
Authors: Coutinho de Oliveira, L. / Volpon, L. / Rahardjo, A.K. / Osborne, M.J. / Culjkovic-Kraljacic, B. / Trahan, C. / Oeffinger, M. / Kwok, B.H. / Borden, K.L.B.
History
DepositionDec 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jun 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 1.6May 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: VPg


Theoretical massNumber of molelcules
Total (without water)21,6571
Polymers21,6571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15800 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein VPg


Mass: 21657.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato virus Y / Production host: Escherichia coli (E. coli) / References: UniProt: A6YPB3, UniProt: A0A1B1UX10*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
171anisotropic12D 1H-15N HSQC
162anisotropic12D 1H-13C HSQC
183anisotropic12D 1H-13C HSQC
111anisotropic23D 1H-15N NOESY
121anisotropic23D 1H-13C NOESY
132anisotropic23D 1H-13C NOESY
143anisotropic24D methyl-methyl 13C-resolved HMQC-NOESY-HMQC
152anisotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1450 uM [U-13C; U-15N] PVY-VPg, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM DTT, 0.02 % v/v sodium azide, 100 uM DSS, 93% H2O/7% D2O15N13C PVY-VPg - H2O93% H2O/7% D2O
solution2450 uM [U-13C; U-15N] PVY-VPg, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM DTT, 0.02 % v/v sodium azide, 100 uM DSS, 100% D2O15N13C PVY-VPg - D2O100% D2O
solution3450 uM ILV labeled PVY-VPg, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM DTT, 0.02 % v/v sodium azide, 100 uM DSS, 93% H2O/10% D2OILV PVY-VPg - H2O93% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMPVY-VPg[U-13C; U-15N]1
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
0.02 % v/vsodium azidenatural abundance1
100 uMDSSnatural abundance1
450 uMPVY-VPg[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
0.02 % v/vsodium azidenatural abundance2
100 uMDSSnatural abundance2
450 uMPVY-VPgILV labeled3
50 mMsodium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
0.02 % v/vsodium azidenatural abundance3
100 uMDSSnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: condition-1 / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8002cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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