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- PDB-6nuj: HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric I... -

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Basic information

Entry
Database: PDB / ID: 6nuj
TitleHIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor BI-224436
ComponentsIntegrase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / HIV / Integrase / inhibitor / allosteric / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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. / Integrase core domain ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L3D / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.10002700303 Å
AuthorsLindenberger, J.J. / Kvaratskhelia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110310 United States
CitationJournal: Elife / Year: 2019
Title: HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors.
Authors: Koneru, P.C. / Francis, A.C. / Deng, N. / Rebensburg, S.V. / Hoyte, A.C. / Lindenberger, J. / Adu-Ampratwum, D. / Larue, R.C. / Wempe, M.F. / Engelman, A.N. / Lyumkis, D. / Fuchs, J.R. / ...Authors: Koneru, P.C. / Francis, A.C. / Deng, N. / Rebensburg, S.V. / Hoyte, A.C. / Lindenberger, J. / Adu-Ampratwum, D. / Larue, R.C. / Wempe, M.F. / Engelman, A.N. / Lyumkis, D. / Fuchs, J.R. / Levy, R.M. / Melikyan, G.B. / Kvaratskhelia, M.
History
DepositionFeb 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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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)18,8862
Polymers18,4441
Non-polymers4431
Water95553
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7724
Polymers36,8872
Non-polymers8852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3500 Å2
ΔGint-21 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.211, 72.211, 66.079
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Integrase /


Mass: 18443.689 Da / Num. of mol.: 1 / Fragment: CCD (UNP residues 50-212) / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F2WR52
#2: Chemical ChemComp-L3D / (2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid / BI 224436


Mass: 442.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26N2O4 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate trihydrate, 0.1 M ammonium sulfate, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→24.3744326678 Å / Num. obs: 12002 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 22.8171075555 Å2 / Rmerge(I) obs: 0.05141 / Rpim(I) all: 0.012 / Rrim(I) all: 0.046 / Net I/σ(I): 61
Reflection shellResolution: 2.1→2.174 Å / Rmerge(I) obs: 0.2756 / Mean I/σ(I) obs: 9.04 / Num. unique obs: 1194 / Rrim(I) all: 0.2873 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-30001.10.1_2155data collection
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6EB2

6eb2


Resolution: 2.10002700303→24.3744326678 Å / SU ML: 0.202846438107 / Cross valid method: FREE R-VALUE / σ(F): 1.33516230696 / Phase error: 25.2615857674
RfactorNum. reflection% reflection
Rfree0.244316687162 2155 10.0111493078 %
Rwork0.219033887173 --
obs0.22167265269 11892 95.5225205236 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.1102107381 Å2
Refinement stepCycle: LAST / Resolution: 2.10002700303→24.3744326678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 33 53 1116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00205987602611087
X-RAY DIFFRACTIONf_angle_d0.6654726412471481
X-RAY DIFFRACTIONf_chiral_restr0.0453051053364165
X-RAY DIFFRACTIONf_plane_restr0.00270709876921177
X-RAY DIFFRACTIONf_dihedral_angle_d15.8311175221613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14880.2717024610121150.246891217191013X-RAY DIFFRACTION73.3420026008
2.1488-2.20260.250922496891310.2312438752871148X-RAY DIFFRACTION85.0964737192
2.2026-2.26210.3123213118521460.2435410424981258X-RAY DIFFRACTION93.8502673797
2.2621-2.32860.2768165336891560.2428159716221349X-RAY DIFFRACTION99.0783410138
2.3286-2.40370.284976249921550.2476878964871304X-RAY DIFFRACTION98.9823609227
2.4037-2.48950.2329556437631440.2394906994541339X-RAY DIFFRACTION97.5657894737
2.4895-2.58910.431786862251530.2422410795981285X-RAY DIFFRACTION97.6238968092
2.5891-2.70680.2884784177811350.2668105946951312X-RAY DIFFRACTION97.4410774411
2.7068-2.84930.2720449191440.2445369386011345X-RAY DIFFRACTION97.896120973
2.8493-3.02750.2612737920471430.234560555041302X-RAY DIFFRACTION97.1755211836
3.0275-3.26070.236295767481480.2276261266091345X-RAY DIFFRACTION98.3530961792
3.2607-3.58790.2739257645041450.2064589069981333X-RAY DIFFRACTION98.9290495315
3.5879-4.1050.1926305588951460.1916153848241340X-RAY DIFFRACTION99.397993311
4.105-5.16370.1565737438061460.1794970263921357X-RAY DIFFRACTION99.0118577075
5.1637-24.37610.2374318360451480.2083454474051341X-RAY DIFFRACTION99.932885906

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