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- PDB-5hot: Structural Basis for Inhibitor-Induced Aggregation of HIV-1 Integrase -

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Basic information

Entry
Database: PDB / ID: 5hot
TitleStructural Basis for Inhibitor-Induced Aggregation of HIV-1 Integrase
ComponentsIntegrase
KeywordsTRANSFERASE/INHIBITOR / integrase / inhibitor complex / nucleic acid binding / DNA integration / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
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 ...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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-2SQ / POL polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.4 Å
AuthorsGupta, K. / Turkki, V. / Sherrill-Mix, S. / Hwang, Y. / Eilers, G. / Taylor, L. / McDanal, C. / Wang, P. / Temelkoff, D. / Nolte, R. ...Gupta, K. / Turkki, V. / Sherrill-Mix, S. / Hwang, Y. / Eilers, G. / Taylor, L. / McDanal, C. / Wang, P. / Temelkoff, D. / Nolte, R. / Velthuisen, E. / Jeffrey, J. / Van Duyne, G.D. / Bushman, F.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI 052845 United States
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 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9874
Polymers65,0802
Non-polymers9072
Water00
1
A: Integrase
B: Integrase
hetero molecules

A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9748
Polymers130,1604
Non-polymers1,8144
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_443-y-1,-x-1,-z-7/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-14 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.060, 107.060, 243.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Integrase


Mass: 32540.080 Da / Num. of mol.: 2 / Mutation: Y15A, F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q72498, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-2SQ / (2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methyl-1-oxo-1,2-dihydroisoquinolin-3-yl]ethanoic acid


Mass: 453.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28FNO5

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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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% 2-methyl-2,4 pentanediol (MPD), 0.1 M sodium citrate pH 5.6 - 6.5
PH range: 5.6-6.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.34→20 Å / Num. obs: 5518 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 5.01 % / Biso Wilson estimate: 180.226 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.069 / Χ2: 0.94 / Net I/σ(I): 17.48 / Num. measured all: 27646
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
4.34-4.450.9220.334.38290428690.37316.1
4.45-4.570.9180.4334.311834152350.48556.6
4.57-4.710.9190.563.8422144244240.623100
4.71-4.850.9520.415.0320913943940.455100
4.85-5.010.9280.3775.0620183863860.419100
5.01-5.190.9610.2856.6620213883870.31899.7
5.19-5.380.9710.3135.8318833633630.348100
5.38-5.60.9710.2447.4518313513510.272100
5.6-5.850.980.2118.0317423393380.23599.7
5.85-6.140.9870.189.3616563253250.201100
6.14-6.470.9860.14211.616213163160.158100
6.47-6.860.9960.10813.414933013000.12199.7
6.86-7.330.9950.08218.0414132802790.09299.6
7.33-7.920.9990.04726.7213122692690.053100
7.92-8.6810.02839.8311972472460.03199.6
8.68-9.70.9990.02153.5210772302280.02499.1
9.7-11.20.9990.02355.459402062030.02698.5
11.2-13.720.9990.02155.27441801770.02498.3
13.72-19.410.0260.86331481470.02299.3
19.4-200.9990.01957.6228796810.02284.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNSrefinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OJR, 1EX4

4ojr

1ex4


Resolution: 4.4→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3576 539 9.6 %Random Selection
Rwork0.3094 4857 --
obs-5396 95.7 %-
Solvent computationBsol: 154.055 Å2
Displacement parametersBiso max: 300 Å2 / Biso mean: 241.48 Å2 / Biso min: 73.34 Å2
Baniso -1Baniso -2Baniso -3
1-27.313 Å20 Å20 Å2
2--27.313 Å20 Å2
3----54.627 Å2
Refinement stepCycle: final / Resolution: 4.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 66 0 3420
Biso mean--229.15 --
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.274
X-RAY DIFFRACTIONc_mcbond_it15.95115
X-RAY DIFFRACTIONc_scbond_it19.67525
X-RAY DIFFRACTIONc_mcangle_it24.77420
X-RAY DIFFRACTIONc_scangle_it29.00130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.4-4.560.4192310.410828031157.4
4.56-4.740.4874540.421491545100
4.74-4.950.5108550.4083489544100
4.95-5.20.4231550.403549555099.8
5.2-5.520.5296550.4217496551100
5.52-5.940.4561560.403551056699.8
5.94-6.520.5991560.3648500556100
6.52-7.420.3715570.287851357099.7
7.42-9.190.3078580.253452458299.7
9.19-200.2409620.246255962198.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6DRGCNS.PAR

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