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- PDB-2k84: Solution Structure of the equine infectious anemia virus p9 GAG p... -

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Basic information

Entry
Database: PDB / ID: 2k84
TitleSolution Structure of the equine infectious anemia virus p9 GAG protein
ComponentsP9
KeywordsVIRAL PROTEIN / polypeptide / Capsid protein / Core protein / Host-virus interaction / Metal-binding / Viral matrix protein / Viral nucleoprotein / Virion / Zinc / Zinc-finger
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding
Similarity search - Function
Gag protein p15 / Gag protein p15 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Gag protein p15 / Gag protein p15 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsSharma, A. / Bruns, K. / Roeder, R. / Henklein, P. / Votteler, J. / Wray, V. / Sharma, U.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Solution structure of the Equine Infectious Anemia Virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein
Authors: Sharma, A. / Bruns, K. / Roder, R. / Henklein, P. / Votteler, J. / Wray, V. / Schubert, U.
History
DepositionSep 2, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 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
A: P9


Theoretical massNumber of molelcules
Total (without water)3,6581
Polymers3,6581
Non-polymers00
Water0
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 the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide P9


Mass: 3658.026 Da / Num. of mol.: 1 / Fragment: UNP residues 457-486 / Source method: obtained synthetically / Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. / References: UniProt: P69732

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 2-3 mM p9 (22-51), 50% H2O/50% CF3CD2OH / Solvent system: 50% H2O/50% CF3CD2OH
SampleConc.: 2 mM / Component: p9 (22-51)
Sample conditionspH: 3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AURELIANeidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerchemical shift assignment
CNS1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Dynamic annealing with NOE constraints using CNS program
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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