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- PDB-3oyd: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -

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Basic information

Entry
Database: PDB / ID: 3oyd
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI GS9160
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


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain ...Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / 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 / Helix non-globular / Ribonuclease H-like superfamily/Ribonuclease H / Special / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Chem-ZZV / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 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
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)101,07616
Polymers99,9444
Non-polymers1,13212
Water4,252236
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)202,15232
Polymers199,8878
Non-polymers2,26524
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area27870 Å2
ΔGint-251 kcal/mol
Surface area57210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.530, 159.530, 123.580
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: 44456.695 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 , 7 types, 248 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ZZV / N-[7-(4-fluorobenzyl)-9-hydroxy-8-oxo-7,8-dihydro-6H-pyrrolo[3,4-g]quinolin-5-yl]-N-methylmethanesulfonamide


Mass: 415.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18FN3O4S
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC / Detector: AREA DETECTOR / Date: Jun 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.54→39.882 Å / Num. obs: 52902 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.108 / Net I/σ(I): 8.5
Reflection shell

Rmerge(I) obs: 0.01

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.54-2.685.51.64211376381.00899.9
2.68-2.845.52.53996472140.641100
2.84-3.045.543769168110.38100
3.04-3.285.56.33502063350.228100
3.28-3.595.59.93239058710.126100
3.59-4.025.513.12938853560.09299.9
4.02-4.645.415.92565247130.08599.8
4.64-5.685.316.12142040100.10899.5
5.68-8.03516.41594331740.05799.5
8.03-39.885518.3885417800.03797.2

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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 3OYB

3oyb


Resolution: 2.54→39.88 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.2112 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8348 / SU B: 7.401 / SU ML: 0.157 / SU R Cruickshank DPI: 0.2348 / SU Rfree: 0.1998 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2669 5.1 %RANDOM
Rwork0.2074 ---
all0.21 ---
obs0.2088 52753 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 140.75 Å2 / Biso mean: 61.9538 Å2 / Biso min: 36.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--1.56 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.54→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 732 68 236 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225394
X-RAY DIFFRACTIONr_angle_refined_deg1.6022.1537511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87223.777188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90415737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0861525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213828
X-RAY DIFFRACTIONr_mcbond_it0.7521.52797
X-RAY DIFFRACTIONr_mcangle_it1.45124568
X-RAY DIFFRACTIONr_scbond_it1.92632597
X-RAY DIFFRACTIONr_scangle_it3.2364.52943
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 191 -
Rwork0.389 3624 -
all-3815 -
obs--99.76 %

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