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Basic information

Entry
Database: PDB / ID: 5oi5
TitleDissociation of biochemical and antiretroviral activities of Integrase-LEDGF Allosteric Inhibitors revealed by resistance of A125 polymorphic HIV-1
ComponentsIntegrase
KeywordsVIRAL PROTEIN / HIV-1 / Integrase / Catalytic core domain
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9VK / Integrase / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRuff, M. / Benarous, R.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration.
Authors: Bonnard, D. / Le Rouzic, E. / Eiler, S. / Amadori, C. / Orlov, I. / Bruneau, J.M. / Brias, J. / Barbion, J. / Chevreuil, F. / Spehner, D. / Chasset, S. / Ledoussal, B. / Moreau, F. / Saib, A. ...Authors: Bonnard, D. / Le Rouzic, E. / Eiler, S. / Amadori, C. / Orlov, I. / Bruneau, J.M. / Brias, J. / Barbion, J. / Chevreuil, F. / Spehner, D. / Chasset, S. / Ledoussal, B. / Moreau, F. / Saib, A. / Klaholz, B.P. / Emiliani, S. / Ruff, M. / Zamborlini, A. / Benarous, R.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5783
Polymers20,1401
Non-polymers4382
Water90150
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1556
Polymers40,2792
Non-polymers8764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3850 Å2
ΔGint-32 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.219, 73.219, 65.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Integrase


Mass: 20139.646 Da / Num. of mol.: 1 / Fragment: Catalytic core domain, UNP Residues 50-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2K7W4, UniProt: P03366*PLUS
#2: Chemical ChemComp-9VK / (2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-2-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid


Mass: 413.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→36.61 Å / Num. obs: 23646 / % possible obs: 89.2 % / Redundancy: 3.2 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LH4

4lh4


Resolution: 2.4→36.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.392 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26131 404 5 %RANDOM
Rwork0.20793 ---
obs0.21072 7673 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.878 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 30 50 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191070
X-RAY DIFFRACTIONr_bond_other_d0.0030.021054
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9711454
X-RAY DIFFRACTIONr_angle_other_deg1.0232407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18724.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.23915177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.09154
X-RAY DIFFRACTIONr_chiral_restr0.1160.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021167
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02236
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0525.008521
X-RAY DIFFRACTIONr_mcbond_other4.9995520
X-RAY DIFFRACTIONr_mcangle_it7.0857.468646
X-RAY DIFFRACTIONr_mcangle_other7.0827.48647
X-RAY DIFFRACTIONr_scbond_it5.1485.651549
X-RAY DIFFRACTIONr_scbond_other5.1465.651549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0148.216809
X-RAY DIFFRACTIONr_long_range_B_refined10.48741.2251242
X-RAY DIFFRACTIONr_long_range_B_other10.48141.0241228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 30 -
Rwork0.157 566 -
obs--99.83 %

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