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Yorodumi- PDB-6v2f: Crystal structure of the HIV capsid hexamer bound to the small mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v2f | ||||||
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Title | Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207 | ||||||
Components | HIV-1 capsid | ||||||
Keywords | VIRAL PROTEIN / HIV capsid / capsid assembly accelerator / long-acting inhibitor / antiviral | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral process / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Appleby, T.C. / Link, J.O. / Yant, S.R. / Villasenor, A.G. / Somoza, J.R. / Hu, E.Y. / Schroeder, S.D. / Cihlar, T. | ||||||
Citation | Journal: Nature / Year: 2020 Title: Clinical targeting of HIV capsid protein with a long-acting small molecule. Authors: Link, J.O. / Rhee, M.S. / Tse, W.C. / Zheng, J. / Somoza, J.R. / Rowe, W. / Begley, R. / Chiu, A. / Mulato, A. / Hansen, D. / Singer, E. / Tsai, L.K. / Bam, R.A. / Chou, C.H. / Canales, E. / ...Authors: Link, J.O. / Rhee, M.S. / Tse, W.C. / Zheng, J. / Somoza, J.R. / Rowe, W. / Begley, R. / Chiu, A. / Mulato, A. / Hansen, D. / Singer, E. / Tsai, L.K. / Bam, R.A. / Chou, C.H. / Canales, E. / Brizgys, G. / Zhang, J.R. / Li, J. / Graupe, M. / Morganelli, P. / Liu, Q. / Wu, Q. / Halcomb, R.L. / Saito, R.D. / Schroeder, S.D. / Lazerwith, S.E. / Bondy, S. / Jin, D. / Hung, M. / Novikov, N. / Liu, X. / Villasenor, A.G. / Cannizzaro, C.E. / Hu, E.Y. / Anderson, R.L. / Appleby, T.C. / Lu, B. / Mwangi, J. / Liclican, A. / Niedziela-Majka, A. / Papalia, G.A. / Wong, M.H. / Leavitt, S.A. / Xu, Y. / Koditek, D. / Stepan, G.J. / Yu, H. / Pagratis, N. / Clancy, S. / Ahmadyar, S. / Cai, T.Z. / Sellers, S. / Wolckenhauer, S.A. / Ling, J. / Callebaut, C. / Margot, N. / Ram, R.R. / Liu, Y.P. / Hyland, R. / Sinclair, G.I. / Ruane, P.J. / Crofoot, G.E. / McDonald, C.K. / Brainard, D.M. / Lad, L. / Swaminathan, S. / Sundquist, W.I. / Sakowicz, R. / Chester, A.E. / Lee, W.E. / Daar, E.S. / Yant, S.R. / Cihlar, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v2f.cif.gz | 296.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v2f.ent.gz | 219.4 KB | Display | PDB format |
PDBx/mmJSON format | 6v2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v2f_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6v2f_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6v2f_validation.xml.gz | 54.7 KB | Display | |
Data in CIF | 6v2f_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/6v2f ftp://data.pdbj.org/pub/pdb/validation_reports/v2/6v2f | HTTPS FTP |
-Related structure data
Related structure data | 3h47S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25592.469 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0, UniProt: P12493*PLUS #2: Chemical | ChemComp-QNG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 12% PEG 3350, 0.2 M sodium thiocyanate, 0.1 M sodium cacodylate, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.92 Å / Num. obs: 105922 / % possible obs: 98.66 % / Redundancy: 5.2 % / Biso Wilson estimate: 29.52 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Rrim(I) all: 0.132 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 10274 / CC1/2: 0.758 / Rpim(I) all: 0.427 / Rrim(I) all: 0.905 / % possible all: 90.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H47 Resolution: 2→29.92 Å / SU ML: 0.2338 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.0908 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.92 Å
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Refine LS restraints |
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LS refinement shell |
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