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- PDB-3hph: Closed tetramer of Visna virus integrase (residues 1-219) in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hph | ||||||
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Title | Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD | ||||||
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![]() | TRANSFERASE / PROTEIN-PROTEIN COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / MAGNESIUM / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / HOST-VIRUS INTERACTION / TRANSCRIPTION / TRANSCRIPTION REGULATION / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION | ||||||
Function / homology | ![]() dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / RNA-directed DNA polymerase activity / exoribonuclease H / exoribonuclease H activity / euchromatin / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral capsid / response to heat / DNA recombination / DNA-binding transcription factor binding / response to oxidative stress / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / transcription coactivator activity / chromatin remodeling / symbiont entry into host cell / viral translational frameshifting / chromatin binding / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hare, S. / Wang, J. / Cherepanov, P. | ||||||
![]() | ![]() Title: Structural basis for functional tetramerization of lentiviral integrase Authors: Hare, S. / Di Nunzio, F. / Labeja, A. / Wang, J. / Engelman, A. / Cherepanov, P. #1: ![]() Title: Application of General Formulas for the Correction of a Lattice Translocation Defect in Crystals of a Lentiviral Integrase in Complex with LEDGF Authors: Hare, S. / Cherepanov, P. / Wang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.3 KB | Display | ![]() |
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PDB format | ![]() | 182.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.1 KB | Display | ![]() |
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Full document | ![]() | 535.3 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hpgSC ![]() 2b4jS 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:
NCS ensembles :
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Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 25090.455 Da / Num. of mol.: 4 Fragment: N-terminal and catalytic domains, UNP residues 923-1039 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 10988.893 Da / Num. of mol.: 4 / Fragment: Integrase binding domain, UNP residues 348-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 121 molecules 






#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2008 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→40 Å / Num. all: 56209 / Num. obs: 55918 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 50.579 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.64→2.71 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 13611 / Num. unique all: 4115 / Num. unique obs: 4092 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HPG and 2B4J Resolution: 2.64→39.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.81 / SU B: 23.978 / SU ML: 0.225 / SU R Cruickshank DPI: 0.425 / SU Rfree: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.01 Å2 / Biso mean: 26.532 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→39.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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