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- PDB-2ari: Solution structure of micelle-bound fusion domain of HIV-1 gp41 -

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Basic information

Entry
Database: PDB / ID: 2ari
TitleSolution structure of micelle-bound fusion domain of HIV-1 gp41
ComponentsEnvelope polyprotein GP160
KeywordsVIRAL PROTEIN / HIV / gp41 / fusion / membrane / protein / micelle / virus
Function / homology
Function and homology information


host cell periphery / virus-mediated perturbation of host defense response => GO:0019049 / : / virion component => GO:0044423 / CD4 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity ...host cell periphery / virus-mediated perturbation of host defense response => GO:0019049 / : / virion component => GO:0044423 / CD4 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsJaroniec, C.P. / Kaufman, J.D. / Stahl, S.J. / Viard, M. / Blumenthal, R. / Wingfield, P.T. / Bax, A.
CitationJournal: Biochemistry / Year: 2005
Title: Structure and Dynamics of Micelle-Associated Human Immunodeficiency Virus gp41 Fusion Domain.
Authors: Jaroniec, C.P. / Kaufman, J.D. / Stahl, S.J. / Viard, M. / Blumenthal, R. / Wingfield, P.T. / Bax, A.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Envelope polyprotein GP160


Theoretical massNumber of molelcules
Total (without water)3,8781
Polymers3,8781
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)30 / 30all calculated structures submitted
RepresentativeModel #1best agreement with measured residual dipolar couplings

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Components

#1: Protein/peptide Envelope polyprotein GP160


Mass: 3878.343 Da / Num. of mol.: 1
Fragment: 30 N-terminal residues, Transmembrane glycoprotein (GP41)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: ENV / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03376, UniProt: P03375*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO; 3D HNCA; 3D HN(CO)CA; 3D HN(CA)CB; 2D HNCG
2223D 15N-separated TOCSY; 3D 15N-separated NOESY; 3D HNHA
1332D IPAP-HSQC JNH; 3D HNCO JNH; 3D QJ-HNCO JNCO; 3D HNCO JCOCA; 3D HN(CO)CA JCACB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Residual dipolar couplings were measured for a peptide-micelle complex aligned with respect to the magnetic field using a ...Text: The structure was determined using triple-resonance NMR spectroscopy. Residual dipolar couplings were measured for a peptide-micelle complex aligned with respect to the magnetic field using a stretched polyacryamide gel.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM HIV-1 gp41 fusion domain U-2H, 13C, 15N; 75 mM sodium dodecyl sulfate; 25 mM sodium phosphate buffer pH 6.5; 0.05% (w/v) sodium azide; 93% H2O, 7% D2O93% H2O/7% D2O
20.7 mM HIV-1 gp41 fusion domain U-15N; 75 mM sodium dodecyl sulfate deuterated; 25 mM sodium phosphate buffer pH 6.5; 0.05% (w/v) sodium azide; 93% H2O, 7% D2O93% H2O/7% D2O
30.7 mM HIV-1 gp41 fusion domain U-2H, 13C, 15N; 75 mM sodium dodecyl sulfate; 25 mM sodium phosphate buffer pH 6.5; 0.05% (w/v) sodium azide; 93% H2O, 7% D2O; sample aligned with respect to the magnetic field using a stretched polyacryalmide gel93% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
175 mM sodium dodecyl sulfate; 25 mM sodium phosphate; 0.05% (w/v) sodium azide 6.5 ambient 298 K
275 mM sodium dodecyl sulfate deuterated; 25 mM sodium phosphate; 0.05% (w/v) sodium azide 6.5 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503
Bruker DRXBrukerDRX8004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR3.5Brukercollection
NMRPipe2.3Delaglioprocessing
NMRPipe2.3Delagliodata analysis
Sparky3.11Goddarddata analysis
X-PLOR-NIH2.9.4Schwietersrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 192 restraints. 57 are residual dipolar coupling (RDC) restraints, 74 are NOE-derived distance restraints, 38 are TALOS-derived loose (minimum +/- 30 ...Details: The structures are based on a total of 192 restraints. 57 are residual dipolar coupling (RDC) restraints, 74 are NOE-derived distance restraints, 38 are TALOS-derived loose (minimum +/- 30 degrees from target value) dihedral angle restraints, and 23 are 3J_HNHA restraints. Note that RDC restraints were included only for the least mobile residues Ile-4 to Met-19 (with S2 > 0.65), dihedral restraints were included for residues Ile-4 to Ala-22, NOE and 3J_HNHA restraints were included for residues Val-2 to Met-24. Also note that the residue index in PDB and constraints files is such that HIV-1 gp41 fusion domain residue i is actually labeled as i+1.
NMR representativeSelection criteria: best agreement with measured residual dipolar couplings
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

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