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- PDB-3l2w: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l2w | ||||||
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Title | Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese and GS9137 (Elvitegravir) | ||||||
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![]() | RECOMBINATION/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / ZINC / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION / RECOMBINATION-DNA complex | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hare, S. / Gupta, S.S. / Cherepanov, P. | ||||||
![]() | ![]() Title: Retroviral intasome assembly and inhibition of DNA strand transfer Authors: Hare, S. / Gupta, S.S. / Valkov, E. / Engelman, A. / Cherepanov, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.2 KB | Display | ![]() |
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PDB format | ![]() | 177 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 897.5 KB | Display | ![]() |
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Full document | ![]() | 911.2 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l2qC ![]() 3l2rC ![]() 3l2uC ![]() 3l2vC ![]() 3oy9C ![]() 3dlrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44456.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5864.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 19 nucleotide preprocessed PFV donor DNA |
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#3: DNA chain | Mass: 5163.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 17 nucleotide preprocessed PFV donor DNA |
-Non-polymers , 5 types, 10 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/ELV.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/ELV.gif)
![](data/chem/img/GOL.gif)
#4: Chemical | ChemComp-ZN / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-NH4 / | #7: Chemical | ChemComp-ELV / | #8: Chemical | ChemComp-GOL / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.46 % / Mosaicity: 0.45 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.35M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50mM Mes-NaOH, pH 6.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Oct 13, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→38.292 Å / Num. all: 26337 / Num. obs: 26337 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.098 |
Reflection shell | Resolution: 3.2→3.37 Å / % possible all: 99.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DLR Resolution: 3.2→35.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 30.126 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.617 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.96 Å2 / Biso mean: 110.3 Å2 / Biso min: 56.82 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→35.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 860 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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