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- PDB-8u6n: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 8u6n
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 3-(2-((6-cyanonaphthalen-1-yl)oxy)phenoxy)-N,N-dimethylpropanamide (JLJ752), a non-nucleoside inhibitor
Components
  • Gag-Pol polyprotein
  • p51 RT
KeywordsVIRAL PROTEIN / REVERSE TRANSCRIPTASE / ANTIVIRAL / DRUG DESIGN / HIV-1
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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. / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / 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
Similarity search - Domain/homology
Chem-VWK / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsPrucha, G. / Henry, S. / Jorgensen, W.L. / Anderson, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH/NAD AI155072 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase.
Authors: Prucha, G.R. / Henry, S. / Hollander, K. / Carter, Z.J. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.S.
History
DepositionSep 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag-Pol polyprotein
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6243
Polymers112,2642
Non-polymers3601
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-22 kcal/mol
Surface area44560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.572, 65.651, 100.573
Angle α, β, γ (deg.)90.00, 114.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gag-Pol polyprotein


Mass: 62224.262 Da / Num. of mol.: 1 / Mutation: C879S, K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Human immunodeficiency virus 1 / References: UniProt: P03366
#2: Protein p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Human immunodeficiency virus 1 / References: UniProt: P03366
#3: Chemical ChemComp-VWK / 3-{2-[(6-cyanonaphthalen-1-yl)oxy]phenoxy}-N,N-dimethylpropanamide


Mass: 360.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM Tris pH 7.5, 15% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.735→91.392 Å / Num. obs: 33124 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 11.2
Reflection shellResolution: 2.735→2.782 Å / Rmerge(I) obs: 1.971 / Num. unique obs: 1630 / CC1/2: 0.344 / Rpim(I) all: 0.906 / Rrim(I) all: 2.354 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→36.45 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.291 1653 5 %
Rwork0.253 --
obs0.255 33076 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 27 8 6757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096931
X-RAY DIFFRACTIONf_angle_d1.0659516
X-RAY DIFFRACTIONf_dihedral_angle_d18.2422325
X-RAY DIFFRACTIONf_chiral_restr0.0551081
X-RAY DIFFRACTIONf_plane_restr0.0091223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.820.40611360.34662570X-RAY DIFFRACTION99
2.82-2.910.42651380.33442585X-RAY DIFFRACTION100
2.91-3.010.39751260.33952617X-RAY DIFFRACTION100
3.01-3.130.40571450.33762622X-RAY DIFFRACTION100
3.13-3.270.38611430.32512565X-RAY DIFFRACTION100
3.27-3.450.35431280.29342633X-RAY DIFFRACTION100
3.45-3.660.33161320.27492616X-RAY DIFFRACTION100
3.66-3.940.2811360.26162594X-RAY DIFFRACTION100
3.94-4.340.26911450.24242636X-RAY DIFFRACTION100
4.34-4.970.26941380.22722622X-RAY DIFFRACTION100
4.97-6.250.29351430.2592641X-RAY DIFFRACTION100
6.25-36.450.24361430.21172722X-RAY DIFFRACTION100

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