+Open data
-Basic information
Entry | Database: PDB / ID: 6vug | ||||||
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Title | Diabody bound to a Reverse Transcriptase Aptamer Complex | ||||||
Components |
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Keywords | PROTEIN BINDING / Aptamer / complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Chesterman, C. / Arnold, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2021 Title: Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Authors: Chesterman, C. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vug.cif.gz | 267 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vug.ent.gz | 203.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/6vug ftp://data.pdbj.org/pub/pdb/validation_reports/vu/6vug | HTTPS FTP |
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-Related structure data
Related structure data | 6vrpC 6vunC 6vuoC 6vupC 7kbmC 7kboC 7kbpC 5d3gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 63875.117 Da / Num. of mol.: 1 / Fragment: p66 subunit, residues 600-1154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 51928.629 Da / Num. of mol.: 1 / Fragment: P51 subunit, residues 168-595 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: A0A076Q3N8, UniProt: P03366*PLUS, RNA-directed DNA polymerase, exoribonuclease H, retroviral ribonuclease H |
-DNA chain , 1 types, 1 molecules E
#5: DNA chain | Mass: 11748.526 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) |
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-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 13249.603 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#4: Antibody | Mass: 13185.589 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 2 types, 12 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-GOL / | |
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-Details
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: 3.69 Å3/Da / Density % sol: 66.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.4 M Ammonium Sulfate 0.1 M HEPES pH 7.8 0.1 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 44085 / % possible obs: 99.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.11 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 1.026 / Num. unique obs: 2070 / Rrim(I) all: 1.171 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D3G Resolution: 3→48.364 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.23 Å2 / Biso mean: 48.5605 Å2 / Biso min: 6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→48.364 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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