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- PDB-3oyi: Crystal structure of the PFV S217Q mutant intasome in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3oyi
TitleCrystal structure of the PFV S217Q mutant intasome in complex with manganese
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
  • PFV integrase
KeywordsRECOMBINATION / VIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / INHIBITOR / DNA-BINDING PROTEIN-DNA complex / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell cytoplasm / viral entry into host cell / host cell nucleus / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease A9 / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / Spumavirus aspartic protease (A9) / Integrase zinc binding domain / Integrase zinc-binding domain / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease A9 / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / Spumavirus aspartic protease (A9) / Integrase zinc binding domain / Integrase zinc-binding domain / Arc Repressor Mutant, subunit A / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Endonuclease III; domain 1 / SH3 type barrels. - #140 / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / RNase H / Integrase core domain / Integrase catalytic domain profile. / Integrase, catalytic core / Ribonuclease H domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / RNase H type-1 domain profile. / Special / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA (> 10) / DNA / AMMONIUM ION / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsHare, S. / Cherepanov, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.
Authors: Hare, S. / Vos, A.M. / Clayton, R.F. / Thuring, J.W. / Cummings, M.D. / Cherepanov, P.
History
DepositionSep 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PFV integrase
B: PFV integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,78014
Polymers100,0264
Non-polymers75410
Water3,693205
1
A: PFV integrase
B: PFV integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules

A: PFV integrase
B: PFV integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,55928
Polymers200,0518
Non-polymers1,50820
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area27460 Å2
ΔGint-221 kcal/mol
Surface area57330 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)160.580, 160.580, 123.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PFV integrase / p42In


Mass: 44497.742 Da / Num. of mol.: 2 / Fragment: UNP residues 752 to 1143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: POL / Plasmid: pSSH6P-PFV-INFL / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P14350

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')


Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA non-transferred strand
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')


Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA transferred strand

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Non-polymers , 6 types, 215 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.72→38.946 Å / Num. obs: 43629 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.146 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.72-2.874.60.8641.62901063100.86499.9
2.87-3.044.70.5332.52773359580.533100
3.04-3.254.70.3343.82633356280.334100
3.25-3.514.70.1975.92470452480.197100
3.51-3.854.70.14282295548510.14299.9
3.85-4.34.70.1189.62084244070.11899.9
4.3-4.974.70.1210.71814938760.1299.4
4.97-6.084.60.13610.61507032900.13699.2
6.08-8.64.30.10511.11121625920.10598
8.6-39.2164.10.08811.8601414690.08896.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OY9
Resolution: 2.72→38.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2516 / WRfactor Rwork: 0.2207 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8322 / SU R Cruickshank DPI: 0.3012 / SU Rfree: 0.2416 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2185 5 %RANDOM
Rwork0.2108 ---
all0.22 ---
obs0.2124 43445 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 138.71 Å2 / Biso mean: 62.1283 Å2 / Biso min: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2--2.29 Å20 Å2
3----4.59 Å2
Refinement stepCycle: LAST / Resolution: 2.72→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 732 38 205 5307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225296
X-RAY DIFFRACTIONr_angle_refined_deg1.6262.1527367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69423.804184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2615734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2291525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213728
X-RAY DIFFRACTIONr_mcbond_it0.6871.52755
X-RAY DIFFRACTIONr_mcangle_it1.32324498
X-RAY DIFFRACTIONr_scbond_it1.71332541
X-RAY DIFFRACTIONr_scangle_it2.944.52869
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 161 -
Rwork0.394 2999 -
all-3160 -
obs--99.87 %

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