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Yorodumi- PDB-4e91: Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+91 | ||||||
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Title | Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BD3 | ||||||
Components | Gag protein | ||||||
Keywords | STRUCTURAL PROTEIN/INHIBITOR / Structural protein Capsid / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lemke, C.T. | ||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein. Authors: Lemke, C.T. / Titolo, S. / von Schwedler, U. / Goudreau, N. / Mercier, J.F. / Wardrop, E. / Faucher, A.M. / Coulombe, R. / Banik, S.S. / Fader, L. / Gagnon, A. / Kawai, S.H. / Rancourt, J. / ...Authors: Lemke, C.T. / Titolo, S. / von Schwedler, U. / Goudreau, N. / Mercier, J.F. / Wardrop, E. / Faucher, A.M. / Coulombe, R. / Banik, S.S. / Fader, L. / Gagnon, A. / Kawai, S.H. / Rancourt, J. / Tremblay, M. / Yoakim, C. / Simoneau, B. / Archambault, J. / Sundquist, W.I. / Mason, S.W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallization via compound-mediated dimerization. Authors: Lemke, C.T. / Titolo, S. / Goudreau, N. / Faucher, A.M. / Mason, S.W. / Bonneau, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e91.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e91.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 4e91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e91_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4e91_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4e91_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4e91_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/4e91 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/4e91 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 133-278 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: Q79791, UniProt: P12497*PLUS #2: Chemical | #3: Chemical | ChemComp-0OF / ( | #4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | |
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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: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.7M Na/K tartrate, 0.1M bis-tris pH7.0, 0.2M NaI, 16% glyerol, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Osmic HiRes2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→57 Å / Num. all: 40348 / Num. obs: 39464 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.37 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.606 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 22.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.77 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→36.606 Å
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Refine LS restraints |
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LS refinement shell |
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