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- PDB-2f76: Solution structure of the M-PMV wild type matrix protein (p10) -

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Basic information

Entry
Database: PDB / ID: 2f76
TitleSolution structure of the M-PMV wild type matrix protein (p10)
ComponentsCore protein p10
KeywordsVIRAL PROTEIN / 4 alpha-helices
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / host cell cytoplasm / viral translational frameshifting / zinc ion binding / metal ion binding
Similarity search - Function
Retroviral GAG p10 protein / 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 / Retrovirus capsid, C-terminal ...Retroviral GAG p10 protein / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / DNA polymerase; domain 1 / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesSimian retrovirus 1
MethodSOLUTION NMR / simulated annealing; molecular dynamics; torsion angle dynamics
AuthorsVlach, J. / Lipov, J. / Veverka, V. / Lang, J. / Srb, P. / Rumlova, M. / Hunter, E. / Ruml, T. / Hrabal, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: D-retrovirus morphogenetic switch driven by the targeting signal accessibility to Tctex-1 of dynein.
Authors: Vlach, J. / Lipov, J. / Rumlova, M. / Veverka, V. / Lang, J. / Srb, P. / Knejzlik, Z. / Pichova, I. / Hunter, E. / Hrabal, R. / Ruml, T.
History
DepositionNov 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Core protein p10


Theoretical massNumber of molelcules
Total (without water)11,9861
Polymers11,9861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average, fewest violations, lowest energy

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Components

#1: Protein Core protein p10 / M-PMV matrix protein


Mass: 11985.779 Da / Num. of mol.: 1 / Fragment: residues 1-100 of Gag polyprotein
Source method: isolated from a genetically manipulated source
Details: A part of Core polyprotein which contains: Core protein p10; Core phosphoprotein pp18; Core protein p12; Core protein p27; Core protein p14; Core protein p4
Source: (gene. exp.) Simian retrovirus 1 / Genus: Betaretrovirus / Species: Mason-Pfizer monkey virus / Gene: gag / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04022, UniProt: P07567*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1 mM matrix protein U-13C, U-15N; 100 mM phosphate buffer (K); 200 mM NaCl; 10 mM DTT; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 800 mM / pH: 6 / Pressure: ambient / Temperature: 298 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
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.3 Rev 2004.184.22.03F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
Sparky3.11T. D. Goddard and D. G. Knellerdata analysis
XPLOR-NIH2.11C.D. Schwieters, J.J. Kuszewski,N. Tjandra and G.M. Clorerefinement
RefinementMethod: simulated annealing; molecular dynamics; torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average, fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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