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- PDB-5hrn: HIV Integrase Catalytic Domain containing F185K mutation complexe... -

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Basic information

Entry
Database: PDB / ID: 5hrn
TitleHIV Integrase Catalytic Domain containing F185K mutation complexed with GSK0002
ComponentsIntegrase
KeywordsTRANSFERASE/INHIBITOR / Viral DNA integration / DNA Binding / LEDGF Binding / VIRAL PROTEIN / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-65P / CACODYLATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsNolte, R.T.
CitationJournal: PLoS Biol. / Year: 2016
Title: Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.
Authors: Gupta, K. / Turkki, V. / Sherrill-Mix, S. / Hwang, Y. / Eilers, G. / Taylor, L. / McDanal, C. / Wang, P. / Temelkoff, D. / Nolte, R.T. / Velthuisen, E. / Jeffrey, J. / Van Duyne, G.D. / Bushman, F.D.
History
DepositionJan 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9687
Polymers17,9401
Non-polymers1,0296
Water2,936163
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,93714
Polymers35,8792
Non-polymers2,05812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5680 Å2
ΔGint-30 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.670, 72.670, 65.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Integrase /


Mass: 17939.508 Da / Num. of mol.: 1 / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: P04585

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-65P / (2S)-tert-butoxy[1-(3,4-difluorobenzyl)-6-methyl-4-(5-methyl-3,4-dihydro-2H-chromen-6-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]acetic acid


Mass: 534.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H32F2N2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Apo crystals grown by Kirsten Kahler in 0.1M Ammonium Sulfate, 0.1M Cacodylate pH 6.5, 7.5% Peg8K, 5mM MgCl, 5mM MnCl, and 5mM DTT ligand soaked for 72 hours in well buffer + 30% eg (cryo) + ...Details: Apo crystals grown by Kirsten Kahler in 0.1M Ammonium Sulfate, 0.1M Cacodylate pH 6.5, 7.5% Peg8K, 5mM MgCl, 5mM MnCl, and 5mM DTT ligand soaked for 72 hours in well buffer + 30% eg (cryo) + 5% DMSO containing 50mM compound

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 9, 2012
RadiationMonochromator: Multilayer Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 21401 / % possible obs: 98.8 % / Redundancy: 9.2 % / Net I/σ(I): 77.95
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
BUSTER2.11.2refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
PHENIXphasing
RefinementResolution: 1.75→18.12 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9313 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 649 3.23 %RANDOM
Rwork0.187 ---
obs0.1882 20070 97.89 %-
Displacement parametersBiso max: 99.34 Å2 / Biso mean: 26.88 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3166 Å20 Å20 Å2
2--0.3166 Å20 Å2
3----0.6333 Å2
Refine analyzeLuzzati coordinate error obs: 0.225 Å
Refinement stepCycle: final / Resolution: 1.75→18.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 58 163 1353
Biso mean--26.15 40.36 -
Num. residues----148
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes181HARMONIC5
X-RAY DIFFRACTIONt_it1242HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion163SEMIHARMONIC5
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_contact1605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1242HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1690HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion2.64
LS refinement shellResolution: 1.75→1.84 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2299 90 3.28 %
Rwork0.2003 2650 -
all0.2012 2740 -
obs--97.89 %
Refinement TLS params.Method: refined / Origin x: -34.7781 Å / Origin y: 4.578 Å / Origin z: 13.7148 Å
111213212223313233
T-0.0679 Å20.0174 Å20.0127 Å2--0.0614 Å20.0048 Å2---0.0909 Å2
L0.7097 °2-0.0624 °20.1669 °2-3.4168 °2-0.5538 °2--1.3403 °2
S0.0315 Å °0.1255 Å °0.0108 Å °-0.4365 Å °-0.1085 Å °-0.1206 Å °0.0156 Å °0.0352 Å °0.077 Å °
Refinement TLS groupSelection details: { A|* }

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