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- PDB-5ldl: Myristoylated T41I/T78I mutant of M-PMV matrix protein -

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Basic information

Entry
Database: PDB / ID: 5ldl
TitleMyristoylated T41I/T78I mutant of M-PMV matrix protein
Componentsmyristoylated M-PMV matrix protein mutant
KeywordsVIRAL PROTEIN / matrix protein / M-PMV / retrovirus
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / nucleic acid binding / viral translational frameshifting / zinc ion binding / metal ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
MYRISTIC ACID / Gag polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
MethodSOLUTION NMR / simulated annealing
AuthorsKroupa, T. / Hrabal, R.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Membrane Interactions of the Mason-Pfizer Monkey Virus Matrix Protein and Its Budding Deficient Mutants.
Authors: Kroupa, T. / Langerova, H. / Dolezal, M. / Prchal, J. / Spiwok, V. / Hunter, E. / Rumlova, M. / Hrabal, R. / Ruml, T.
History
DepositionJun 27, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJul 27, 2016ID: 2MXI
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: myristoylated M-PMV matrix protein mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9662
Polymers14,7381
Non-polymers2281
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10560 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein myristoylated M-PMV matrix protein mutant / Core polyprotein


Mass: 14737.740 Da / Num. of mol.: 1 / Mutation: T41I, T78I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07567
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D CBCA(CO)NH
122anisotropic12D 1H-15N HSQC IPAP
131isotropic13D HN(CA)CB
141isotropic13D (H)CCH-TOCSY
151isotropic13D 1H-13C NOESY
161isotropic13D 1H-15N NOESY
171isotropic13D HNCA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] myristoylated retroviral matrix protein, 100 mM phosphate, 300 mM sodium choride, 5 mM DTT, 90% H2O/10% D2O15N/13C_sample90% H2O/10% D2O
filamentous virus2400 mM [U-15N] myristoylated retroviral matrix protein, 50 mM phosphate, 150 mM sodium choride, 5 mM DTT, 10 mg/mL Pf1 phage, 90% H2O/10% D2ORDC_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMmyristoylated retroviral matrix protein[U-13C; U-15N]1
100 mMphosphatenone1
300 mMsodium choridenone1
5 mMDTTnone1
400 mMmyristoylated retroviral matrix protein[U-15N]2
50 mMphosphatenone2
150 mMsodium choridenone2
5 mMDTTnone2
10 mg/mLPf1 phagenone2
Sample conditionsIonic strength: 600 mM / Label: conditions / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNpeak picking
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 30

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