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Yorodumi- PDB-2xv6: Crystal structure of the HIV-1 capsid protein C-terminal domain (... -
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-Basic information
Entry | Database: PDB / ID: 2xv6 | ||||||
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Title | Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH. | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information 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 ...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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 VICUGNA PACOS (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A. | ||||||
Citation | Journal: To be Published Title: Targeting HIV-1 Virion Formation with Nanobodies -Implications for the Design of Assembly Inhibitors Authors: Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xv6.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xv6.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xv6_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 2xv6_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 2xv6_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 2xv6_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xv6 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xv6 | HTTPS FTP |
-Related structure data
Related structure data | 2xt1SC 2xxcC 2xxmC C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 8455.631 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 278-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4-3 / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: P12497 #2: Antibody | Mass: 13213.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VICUGNA PACOS (alpaca) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) #3: Water | ChemComp-HOH / | Sequence details | THE VHH RESIDUES (CHAIN B AND D) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. 6XHISTIDINE C- ...THE VHH RESIDUES (CHAIN B AND D) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. 6XHISTIDINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 45.973 % / Description: NONE |
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Crystal grow | Details: 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2008 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→47.63 Å / Num. obs: 42152 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.83 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.6 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XT1 Resolution: 1.89→37.34 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.149 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.119 Details: THE 6XHISTIDINE TAG AT THE C-TERMINUS IS DISORDERED.
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Displacement parameters | Biso mean: 27.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.182 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→37.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.96 Å / Total num. of bins used: 15
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