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- PDB-2jmg: Solution structure of V7R mutant of HIV-1 myristoylated matrix protein -

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Basic information

Entry
Database: PDB / ID: 2jmg
TitleSolution structure of V7R mutant of HIV-1 myristoylated matrix protein
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / V7R mutant of HIV-1 myristoylated matrix protein
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MYRISTIC ACID / Gag protein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / distance geometry
AuthorsSaad, J.S. / Loeliger, E. / Luncsford, P. / Liriano, M. / Tai, J. / Kim, A. / Miller, J. / Joshi, A. / Freed, E.O. / Summers, M.F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Point mutations in the HIV-1 matrix protein turn off the myristyl switch.
Authors: Saad, J.S. / Loeliger, E. / Luncsford, P. / Liriano, M. / Tai, J. / Kim, A. / Miller, J. / Joshi, A. / Freed, E.O. / Summers, M.F.
History
DepositionNov 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0212
Polymers14,7931
Non-polymers2281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Gag polyprotein


Mass: 14792.679 Da / Num. of mol.: 1 / Fragment: MATRIX DOMAIN, RESIDUES 2-132 / Mutation: V7R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / References: UniProt: Q72497, UniProt: Q6E183*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-1H NOESY
1313D HNCA
1413D HN(CO)CA
1523D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C, U-100% 15N] HIV-1 V7R-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2Osample_190% H2O/10% D2O
solution21 mM [U-100% 15N] HIV-1 V7R-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2Osample_290% H2O/10% D2O
solution31 mM HIV-1 V7R-myrMA, 50 mM Sodium phosphate, 100 mM NaCl, 5 mM DTT, 90% H2O, 10% D2Osample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHIV-1 V7R-myrMA[U-100% 13C; U-100% 15N]1
1 mMHIV-1 V7R-myrMA[U-100% 15N]2
1 mMHIV-1 V7R-myrMAnatural abundance3
50 mMSodium phosphatenatural abundance1
50 mMSodium phosphatenatural abundance2
50 mMSodium phosphatenatural abundance3
100 mMNaClnatural abundance1
100 mMNaClnatural abundance2
100 mMNaClnatural abundance3
5 mMDTTnatural abundance1
5 mMDTTnatural abundance2
5 mMDTTnatural abundance3
Sample conditionspH: 5.5 / 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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