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- PDB-6rwg: Structure of HIV-1 CAcSP1NC mutant(W41A,M42A) interacting with ma... -

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Basic information

Entry
Database: PDB / ID: 6rwg
TitleStructure of HIV-1 CAcSP1NC mutant(W41A,M42A) interacting with maturation inhibitor EP39
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / GAG / HIV-1 / maturation inhibitor / EP39 / Structural Genomics / PSI-Biology / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / 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 / Retrovirus capsid, C-terminal ...Retroviral nucleocapsid Gag protein p24, N-terminal / 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 / 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
Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsChen, X. / Coric, P. / Larue, V. / Nonin-Lecomte, S. / Bouaziz, S. / Structural Genomics Consortium (SGC)
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)201603250053 China
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: The HIV-1 maturation inhibitor, EP39, interferes with the dynamic helix-coil equilibrium of the CA-SP1 junction of Gag.
Authors: Chen, X. / Coric, P. / Larue, V. / Turcaud, S. / Wang, X. / Nonin-Lecomte, S. / Bouaziz, S.
History
DepositionJun 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)17,5773
Polymers17,4461
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, The structure of NCp7 is known to bind 2 zincs atoms to form zinc fingers as published previously.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12680 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Gag polyprotein


Mass: 17446.146 Da / Num. of mol.: 1 / Mutation: W41A, M42A
Source method: isolated from a genetically manipulated source
Details: every model has chain A,B and C. Chain A contains 157 amino acids. Chain B and chain C are zinc atoms. 2 zinc atoms bind to NC and form 2 zinc fingers.
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: E7DAY8, UniProt: P12493*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D NOESY-HSQC
131isotropic13D TOCSY-HSQC
141isotropic13D HNHA

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Sample preparation

DetailsType: solution / Contents: 300 uM [U-15N] HIV-1 CAcSP1NC, 90% H2O/10% D2O
Details: buffer: 25mM sodium acetate; 25mM NaCl; 0.1mM ZnCl2;0.1mM BME. pH 6.5
Label: 15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: HIV-1 CAcSP1NC / Isotopic labeling: [U-15N]
Sample conditionsIonic strength: 25 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryo-probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5 pl 7Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
TALOSCornilescu, Delaglio and Baxdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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