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- PDB-4ojr: Crystal Structure of the HIV-1 Integrase catalytic domain with GSK1264 -

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Basic information

Entry
Database: PDB / ID: 4ojr
TitleCrystal Structure of the HIV-1 Integrase catalytic domain with GSK1264
ComponentsHIV-1 Integrase
KeywordsVIRAL PROTEIN / Viral DNA integration / DNA Binding / LEDGF Binding
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2SQ / CACODYLATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsGupta, K. / Brady, T. / Dyer, B. / Hwang, Y. / Male, F. / Nolte, R.T. / Wang, L. / Velthuisen, E. / Jeffrey, J. / Van Duyne, G. / Bushman, F.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Allosteric Inhibition of Human Immunodeficiency Virus Integrase: LATE BLOCK DURING VIRAL REPLICATION AND ABNORMAL MULTIMERIZATION INVOLVING SPECIFIC PROTEIN DOMAINS.
Authors: Gupta, K. / Brady, T. / Dyer, B.M. / Malani, N. / Hwang, Y. / Male, F. / Nolte, R.T. / Wang, L. / Velthuisen, E. / Jeffrey, J. / Van Duyne, G.D. / Bushman, F.D.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7635
Polymers17,9401
Non-polymers8244
Water1,820101
1
A: HIV-1 Integrase
hetero molecules

A: HIV-1 Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52610
Polymers35,8792
Non-polymers1,6478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4650 Å2
ΔGint-35 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.664, 72.664, 65.453
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 / Integrase / IN


Mass: 17939.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1209-1371 / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HIV-1B1 / Gene: gag-pol / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: P03366
#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.: 1 / Source method: obtained synthetically / Formula: C26H28FNO5
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


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


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% Peg 8K, 0.2M Ammonium Sulfate, 0.1M sodiium cacodylate pH 6.5, 5mM MgCl2, 5mM MnCl2, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 18314 / Num. obs: 17966 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.044 / Χ2: 1.029 / Net I/σ(I): 18.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.82-1.898.50.4117461.134198
1.89-1.968.50.28917751.263197.9
1.96-2.058.50.17717480.993197.6
2.05-2.168.40.1317860.981198.6
2.16-2.298.40.09717781.031198.3
2.29-2.478.50.07117900.949198.5
2.47-2.728.40.0618171.035198.7
2.72-3.118.30.04818060.936198.9
3.11-3.928.10.03618430.936198.9
3.92-507.50.03318771.027196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→28.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.2314 / WRfactor Rwork: 0.2133 / FOM work R set: 0.8623 / SU B: 4.11 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1046 / SU Rfree: 0.0954 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.105 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 572 3.2 %RANDOM
Rwork0.1889 ---
obs0.1893 17396 98.24 %-
all-18314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 42.944 Å2 / Biso min: 14.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.29 Å2-0 Å2
2--0.29 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.82→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 44 101 1128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191070
X-RAY DIFFRACTIONr_bond_other_d0.0010.021024
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9311460
X-RAY DIFFRACTIONr_angle_other_deg0.7313.0022335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8395135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21125.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.715152
X-RAY DIFFRACTIONr_chiral_restr0.070.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
X-RAY DIFFRACTIONr_mcbond_it1.2812.558529
X-RAY DIFFRACTIONr_mcbond_other1.2822.55528
X-RAY DIFFRACTIONr_mcangle_it2.1443.808658
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 43 -
Rwork0.229 1250 -
all-1293 -
obs--97.66 %
Refinement TLS params.Method: refined / Origin x: -35.861 Å / Origin y: 4.999 Å / Origin z: 13.928 Å
111213212223313233
T0.1051 Å20.0212 Å20.0067 Å2-0.1078 Å20.0091 Å2--0.0125 Å2
L1.0367 °2-0.0509 °20.1641 °2-4.7774 °20.0866 °2--1.5561 °2
S0.0041 Å °0.1482 Å °0.0299 Å °-0.5007 Å °-0.0325 Å °-0.0937 Å °0.0264 Å °0.0122 Å °0.0284 Å °

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