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- PDB-4jlh: HIV-1 Integrase Catalytic Core Domain A128T Mutant Complexed with... -

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Basic information

Entry
Database: PDB / ID: 4jlh
TitleHIV-1 Integrase Catalytic Core Domain A128T Mutant Complexed with Allosteric Inhibitor
ComponentsHIV-1 Integrase catalytic core domain
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Integrase / CCD / DDE motif / drug resistance / A128T mutation / dimer interface / allosteric inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family 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-0L9 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsFeng, L. / Kvaratskhelia, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The A128T Resistance Mutation Reveals Aberrant Protein Multimerization as the Primary Mechanism of Action of Allosteric HIV-1 Integrase Inhibitors.
Authors: Feng, L. / Sharma, A. / Slaughter, A. / Jena, N. / Koh, Y. / Shkriabai, N. / Larue, R.C. / Patel, P.A. / Mitsuya, H. / Kessl, J.J. / Engelman, A. / Fuchs, J.R. / Kvaratskhelia, M.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: HIV-1 Integrase catalytic core domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6993
Polymers18,1821
Non-polymers5172
Water79344
1
A: HIV-1 Integrase catalytic core domain
hetero molecules

A: HIV-1 Integrase catalytic core domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3986
Polymers36,3652
Non-polymers1,0334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3780 Å2
ΔGint-38 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.210, 72.210, 65.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein HIV-1 Integrase catalytic core domain


Mass: 18182.473 Da / Num. of mol.: 1 / Mutation: A128T, F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497
#2: Chemical ChemComp-0L9 / (2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid


Mass: 420.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15BrClNO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na Cacodylate, 1.4 M Na Acetate, pH 6.5, Vapor Diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 7, 2013 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.09→62.54 Å / Num. all: 12121 / Num. obs: 12058 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.034 / Χ2: 1.806 / Net I/σ(I): 33.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.133.90.4676121.61199.8
2.13-2.163.90.4365861.6591100
2.16-2.2140.3145911.7191100
2.21-2.253.90.2525901.7721100
2.25-2.340.2255961.7541100
2.3-2.3540.1826011.708199.8
2.35-2.4140.1495991.697199.8
2.41-2.4840.1335911.6451100
2.48-2.5540.16041.6961100
2.55-2.6340.0916041.8561100
2.63-2.7340.0716041.8251100
2.73-2.8440.0595871.7461100
2.84-2.974.10.0486071.851100
2.97-3.1240.0416081.9211100
3.12-3.3240.0376081.969199.5
3.32-3.5740.0325991.941199.7
3.57-3.9340.0316121.948198.6
3.93-4.540.0286021.868197.3
4.5-5.673.90.0276131.926196.7
5.67-503.70.0236441.985196

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.25 Å
Translation2.5 Å28.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2534 / WRfactor Rwork: 0.2091 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8432 / SU B: 8.568 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1755 / SU Rfree: 0.1653 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 575 4.8 %RANDOM
Rwork0.1984 ---
obs0.2004 11995 98.96 %-
all-11420 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 212.06 Å2 / Biso mean: 60.2756 Å2 / Biso min: 36.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 30 44 1164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221139
X-RAY DIFFRACTIONr_angle_refined_deg1.61.971533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3965133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17224.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.77315191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.816154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02816
X-RAY DIFFRACTIONr_mcbond_it0.9281.5684
X-RAY DIFFRACTIONr_mcangle_it1.77921093
X-RAY DIFFRACTIONr_scbond_it2.6143454
X-RAY DIFFRACTIONr_scangle_it4.3294.5440
LS refinement shellResolution: 2.09→2.145 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 48 -
Rwork0.271 831 -
all-879 -
obs--99.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.48170.53560.13963.1746-0.20881.71010.0834-0.0841-0.02720.228-0.1824-0.0731-0.15310.01110.0990.1949-0.01330.00570.2003-0.01750.1518-35.319310.0547-5.9757
2-0.4525-1.0551.00194.93963.20421.4537-0.2149-0.26050.57472.2633-0.9410.55520.8972-1.39921.15590.9911-0.13770.31950.5537-0.19610.2726-39.04979.51883.4999
36.5626-2.31331.38094.7427-0.2843.32060.134-0.2454-0.14130.5276-0.14670.38750.3139-0.34050.01270.305-0.10170.04880.2593-0.01880.2006-41.8485-4.4142-0.6373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 135
2X-RAY DIFFRACTION2A136 - 159
3X-RAY DIFFRACTION3A160 - 209

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