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- PDB-2lyb: Structure of HIV-1 myr(-) matrix protein in complex with 1,2-dioc... -

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Basic information

Entry
Database: PDB / ID: 2lyb
TitleStructure of HIV-1 myr(-) matrix protein in complex with 1,2-dioctanoyl-sn-phosphatidyl-L-serine
ComponentsMatrix protein p17
KeywordsVIRAL PROTEIN / Gag / matrix / plasma membrane / lipid
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / 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 / 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 ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / DNA polymerase; domain 1 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8SP / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsVlach, J. / Saad, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Trio engagement via plasma membrane phospholipids and the myristoyl moiety governs HIV-1 matrix binding to bilayers.
Authors: Vlach, J. / Saad, J.S.
History
DepositionSep 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0752
Polymers15,5631
Non-polymers5121
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 the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrix protein p17 / MA / Gag-Pol polyprotein


Mass: 15563.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: NEW YORK-5 ISOLATE / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P12497
#2: Chemical ChemComp-8SP / O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine


Type: L-peptide linking / Mass: 511.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H42NO10P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-edited/13C-filtered NOESY
1213D (H)CCH-TOCSY
1312D 1H-13C HSQC
1423D HNCA
1523D HN(CO)CA
1623D HN(CA)CB
1723D CBCA(CO)NH
1823D 1H-15N TOCSY
1923D 1H-15N NOESY
11013D 1H-13C NOESY
11122D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-95% 13C] MA, 0.8-1.0 mM 1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.4-1.0 mM [U-95% 13C; U-95% 15N] MA, 0.8-1.0 mM 1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.4 mMMA-1[U-95% 13C]1
mM1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt-20.8-1.01
50 mMsodium phosphate-31
2 mMDTT-41
mMMA-5[U-95% 13C; U-95% 15N]0.4-1.02
mM1,2-dioctanoyl-sn-glycero-3-phospho-L-serine, sodium salt-60.8-1.02
50 mMsodium phosphate-72
2 mMDTT-82
Sample conditionsIonic strength: 50 / pH: 5.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPN_AnalysisCCPNdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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