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- PDB-5irt: Dimerization interface of the noncrystalline HIV-1 capsid protein... -

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Basic information

Entry
Database: PDB / ID: 5irt
TitleDimerization interface of the noncrystalline HIV-1 capsid protein lattice from solid state NMR spectroscopy of tubular assemblies
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / tubular assembly / symmetric dimer / noncrystalline lattice / supramolecular structure
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodSOLID-STATE NMR / simulated annealing
AuthorsBayro, M.J. / Tycko, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
ional Institutes of Health Intramural AIDS targeted Anti-viral Program United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies.
Authors: Bayro, M.J. / Tycko, R.
History
DepositionMar 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection / Structure summary
Category: entity / pdbx_audit_support / pdbx_nmr_software
Item: _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name
Revision 1.4Jun 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 1.5May 15, 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

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Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)51,2612
Polymers51,2612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Capsid protein p24


Mass: 25630.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Strain: isolate NY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12493

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic113C-13C 2D correlation
121isotropic1NCACX 2D correlation
131isotropic1NCOCX 2D correlation
142isotropic113C-13C 2D correlation
153isotropic113C-13C 2D correlation
163isotropic1NCACX 2D correlation
174isotropic2LGCP 1H-13C 1D buildup
184isotropic2LGCP 1H-15N 1D buildup
194isotropic1Intermolecular REDOR
1105isotropic1Side-chain/backbone REDOR
1111isotropic2BroBaRR 13C-13C buildup
1123isotropic1Vector angle Trp Ca-N/Cd1-Ne1

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid115 mM U-15N,13C-Met and U-15N Capsid protein, waterWild-type CAMet_15Nwater
solid215 mM 2-13C-glycerol and U-15N Capsid protein, water2-13C-glycerol and U-15N2glyc_15Nwater
solid315 mM 2-13C-glycerol, U-15N, unlabeled Tyr and Phe Capsid protein, water2-13C-glycerol, U-15N, unlabeled Tyr and unlabeled Phe2glyc_15N_revYFwater
solid47.5 mM Methyl-13C-Met Capsid protein-1, 7.5 mM 15N-indole Capsid protein-2, waterMethyl-13C-Met sample mixed with 15N-indole sample (1:1 mixture). Trp 15N labeled at Ne1 position only.Met13C_Trp15N_mixwater
solid515 mM Methyl-13C-Met, 2-13C-indole, U-15N Capsid protein, waterMethyl-13C-Met, 2-13C-indole, and U-15N. Trp 13C labeled at Cd1 position.Met13C_Trp13C_U15Nwater
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mMCapsid proteinU-15N,13C-Met and U-15N1
15 mMCapsid protein2-13C-glycerol and U-15N2
15 mMCapsid protein2-13C-glycerol, U-15N, unlabeled Tyr and Phe3
7.5 mMCapsid protein-1Methyl-13C-Met4
7.5 mMCapsid protein-215N-indole4
15 mMCapsid proteinMethyl-13C-Met, 2-13C-indole, U-15N5
Sample conditionsDetails: Solvent contained 50 mM Tris pH 8.0 and 1 M NaCl. Same condition used for all samples.
Ionic strength: 1 M / Label: sample_condition / pH: 8.0 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian InfinityVarianInfinity60013.2 mm BioMAS Varian probe
Varian InfinityVarianInfinity75023.2 mm E-free Bruker probe

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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