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- PDB-2kgf: N-terminal domain of capsid protein from the Mason-Pfizer monkey virus -

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Basic information

Entry
Database: PDB / ID: 2kgf
TitleN-terminal domain of capsid protein from the Mason-Pfizer monkey virus
ComponentsCapsid protein p27
KeywordsVIRAL PROTEIN / Retrovirus capsid protein / N-terminal core domain (SCOP) / Capsid protein
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / nucleic acid binding / zinc ion binding / metal ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 / 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
Biological speciesMason-Pfizer monkey virus
MethodSOLUTION NMR / simulated annealing
AuthorsMacek, P. / Chmelik, J. / Zidek, L. / Kaderavek, P. / Padrta, P. / Ruml, T. / Pichova, I. / Rumlova, M. / Sklenar, V.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: NMR structure of the N-terminal domain of capsid protein from the mason-pfizer monkey virus
Authors: Macek, P. / Chmelik, J. / Krizova, I. / Kaderavek, P. / Padrta, P. / Zidek, L. / Wildova, M. / Hadravova, R. / Chaloupkova, R. / Pichova, I. / Ruml, T. / Rumlova, M. / Sklenar, V.
#1: Journal: Biomol.Nmr Assign. / Year: 2008
Title: 1H, 13C, and 15N resonance assignment of the N-terminal domain of Mason-Pfizer monkey virus capsid protein, CA 1-140
Authors: Macek, P. / Zidek, L. / Rumlova, M. / Pichova, I. / Sklenar, V.
History
DepositionMar 10, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p27


Theoretical massNumber of molelcules
Total (without water)15,4701
Polymers15,4701
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)50 / 15010 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Capsid protein p27 /


Mass: 15470.034 Da / Num. of mol.: 1 / Fragment: UNP residues 300-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07567

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY
172IPAP [15N, 1H]‑HSQC
182HN[C]-S3E
1922D IPAP [13C', 1H]-HCACO (C' detected)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.0 mM [U-100% 13C; U-100% 15N] MPMV NTD CA, 90% H2O, 10% D2O90% H2O/10% D2O
20.7-1.0 mM [U-100% 13C; U-100% 15N] MPMV NTD CA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMMPMV NTD CA[U-100% 13C; U-100% 15N]1
0.7 mMMPMV NTD CA[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 150mM NaCl / pH: 8.0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSGoddardchemical shift assignment
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2246 / NOE intraresidue total count: 836 / NOE long range total count: 445 / NOE medium range total count: 450 / NOE sequential total count: 515 / Hydrogen bond constraints total count: 124 / Protein phi angle constraints total count: 107 / Protein psi angle constraints total count: 107
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 10 structures for lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 50 / Representative conformer: 1

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