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- PDB-2k4e: Solution structure of the HIV-2 UNMYRISTOYLATED MATRIX PROTEIN -

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Basic information

Entry
Database: PDB / ID: 2k4e
TitleSolution structure of the HIV-2 UNMYRISTOYLATED MATRIX PROTEIN
ComponentsHIV-2 unmyristoylated matrix protein
KeywordsSTRUCTURAL PROTEIN / AIDS / CAPSID PROTEIN / MYRISTATE / MATRIX / GAG / HIV / VIRION / PLASMA MEMBRANE
Function / homology
Function and homology information


HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression ...HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / DNA polymerase; domain 1 / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 2
MethodSOLUTION NMR / distance geometry
AuthorsSaad, J.S. / Ablan, S.D. / Ghanam, R.H. / Kim, A. / Andrews, K. / Nagashima, K. / Freed, E.O. / Summers, M.F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the myristylated human immunodeficiency virus type 2 matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in membrane targeting.
Authors: Saad, J.S. / Ablan, S.D. / Ghanam, R.H. / Kim, A. / Andrews, K. / Nagashima, K. / Soheilian, F. / Freed, E.O. / Summers, M.F.
History
DepositionJun 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: 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: HIV-2 unmyristoylated matrix protein


Theoretical massNumber of molelcules
Total (without water)14,8991
Polymers14,8991
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 / 50target function
RepresentativeModel #1fewest violations

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Components

#1: Protein HIV-2 unmyristoylated matrix protein / Matrix protein p17


Mass: 14899.256 Da / Num. of mol.: 1 / Fragment: UNP residues 2 to 135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 2 / Strain: pROD10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04584

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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 1H-15N NOESY
1322D 1H-1H NOESY
1433D HNCA
1533D HN(CO)CA
1613D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-15N] HIV-2 unmyristoylated matrix protein, 20 mM potassium phosphate, 10 mM DTT, 50 mM Glutamate, 50 mM Aspartate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM HIV-2 unmyristoylated matrix protein, 100% D2O100% D2O
30.8 mM [U-13C; U-15N] HIV-2 unmyristoylated matrix protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMHIV-2 unmyristoylated matrix protein[U-15N]1
20 mMpotassium phosphate1
10 mMDTT1
50 mMGlutamate1
50 mMAspartate1
100 mMsodium chloride1
0.8 mMHIV-2 unmyristoylated matrix protein2
0.8 mMHIV-2 unmyristoylated matrix protein[U-13C; U-15N]3
Sample conditionsIonic strength: 0.1 / pH: 6.3 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR softwareName: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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