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- PDB-5uop: CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2-... -

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Entry
Database: PDB / ID: 5uop
TitleCRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 18)
Components
  • (NUCLEOTIDE PREPROCESSED PFV DONOR DNA ...) x 2
  • INTEGRASE
KeywordsTRANSFERASE/DNA/INHIBITOR / DNA INTEGRATION / VIRAL PROTEIN / RECOMBINATION-INHIBITOR-DNA COMPLEX / TRANSFERASE-DNA-INHIBITOR COMPLEX
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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
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 / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / 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 (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase domain 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
Chem-8G4 / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsKlein, D.J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV.
Authors: Schreier, J.D. / Embrey, M.W. / Raheem, I.T. / Barbe, G. / Campeau, L.C. / Dubost, D. / McCabe Dunn, J. / Grobler, J. / Hartingh, T.J. / Hazuda, D.J. / Klein, D. / Miller, M.D. / Moore, K.P. ...Authors: Schreier, J.D. / Embrey, M.W. / Raheem, I.T. / Barbe, G. / Campeau, L.C. / Dubost, D. / McCabe Dunn, J. / Grobler, J. / Hartingh, T.J. / Hazuda, D.J. / Klein, D. / Miller, M.D. / Moore, K.P. / Nguyen, N. / Pajkovic, N. / Powell, D.A. / Rada, V. / Sanders, J.M. / Sisko, J. / Steele, T.G. / Wai, J. / Walji, A. / Xu, M. / Coleman, P.J.
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE
B: INTEGRASE
C: NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)
D: NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,39817
Polymers99,9444
Non-polymers1,45413
Water3,243180
1
A: INTEGRASE
B: INTEGRASE
C: NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)
D: NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)
hetero molecules

A: INTEGRASE
B: INTEGRASE
C: NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)
D: NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,79534
Polymers199,8878
Non-polymers2,90826
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area29150 Å2
ΔGint-292 kcal/mol
Surface area55460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.818, 158.818, 123.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 INTEGRASE / Pr125Pol


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Gene: pol / Production host: Escherichia coli (E. coli)
References: UniProt: P14350, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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NUCLEOTIDE PREPROCESSED PFV DONOR DNA ... , 2 types, 2 molecules CD

#2: DNA chain NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)


Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human spumaretrovirus
#3: DNA chain NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)


Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human spumaretrovirus

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Non-polymers , 6 types, 193 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-8G4 / (1S,2S,5R)-8'-[(3-chloro-4-fluorophenyl)methyl]-2'-[2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl]-6'-hydroxy-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione


Mass: 566.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24ClFN4O6
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.91 Å3/Da / Density % sol: 68.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.25 M AMMONIUM SULFATE, 25% (V/V)GLYCEROL, 4.8% (V/V) 1,6-HEXANEDIOL, 50 MM MES-NAOH, 1MM EDTA, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.846→159 Å / Num. obs: 37741 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 94.19 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 17
Reflection shellResolution: 2.85→2.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.619 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 2.85→36.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1876 5 %RANDOM
Rwork0.183 ---
obs0.184 37490 100 %-
Displacement parametersBiso mean: 78.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.1572 Å20 Å20 Å2
2---0.1572 Å20 Å2
3---0.3144 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.85→36.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 732 89 180 5333
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015355HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1682SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC8
X-RAY DIFFRACTIONt_gen_planes707HARMONIC8
X-RAY DIFFRACTIONt_it5355HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.15
X-RAY DIFFRACTIONt_other_torsion21.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion702SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6220SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.294 165 5.78 %
Rwork0.232 2689 -
all0.235 2854 -
obs--99.83 %

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