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Yorodumi- PDB-8gdv: Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gdv | |||||||||
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Title | Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 capsid / IP6 / CPSF6 | |||||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / virion membrane / structural molecule activity / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Briganti, L. / Schope, L. / Kvaratskhelia, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6 Authors: Huang, S. / Briganti, L. / Kvaratskhelia, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gdv.cif.gz | 499.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gdv.ent.gz | 417.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/8gdv ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gdv | HTTPS FTP |
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-Related structure data
Related structure data | 7snqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25443.234 Da / Num. of mol.: 6 / Mutation: A14C, E45C, W184A, M185A, M66I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2ECD8 #2: Protein/peptide | Mass: 1550.796 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) #3: Chemical | Has ligand of interest | N | |
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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: 2.81 Å3/Da / Density % sol: 60.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M Tris hydrochloride, 11% PEG 8000, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jul 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→47.88 Å / Num. obs: 27382 / % possible obs: 95.37 % / Redundancy: 7.4 % / Biso Wilson estimate: 71.48 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.1312 / Net I/σ(I): 6.56 |
Reflection shell | Resolution: 3.3→3.418 Å / Mean I/σ(I) obs: 1.41 / Num. unique obs: 2733 / CC1/2: 0.798 / % possible all: 97.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7SNQ Resolution: 3.3→47.88 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→47.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.6463 Å / Origin y: 19.7585 Å / Origin z: 46.6826 Å
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Refinement TLS group | Selection details: all |