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- PDB-4kko: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4kko
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-((4-methoxy-6-(2-morpholinoethoxy)-1,3,5-triazin-2-yl)amino)-2-((3-methylbut-2-en-1-yl)oxy)benzonitrile (JLJ513), a non-nucleoside inhibitor
Components
  • HIV-1 reverse transcriptase, p51 subunit
  • HIV-1 reverse transcriptase, p66 subunit
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Polymerase / Transferase / Hydrolase/inhibitor / Rnase / HYDROLASE-HYDROLASE INHIBITOR complex
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 / RNA-directed DNA polymerase / establishment of integrated proviral latency / 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 / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / 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 / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H 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. / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1RE / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsFrey, K.M. / Anderson, K.S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Extension into the entrance channel of HIV-1 reverse transcriptase-Crystallography and enhanced solubility.
Authors: Bollini, M. / Frey, K.M. / Cisneros, J.A. / Spasov, K.A. / Das, K. / Bauman, J.D. / Arnold, E. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 reverse transcriptase, p66 subunit
B: HIV-1 reverse transcriptase, p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4713
Polymers114,0292
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-30 kcal/mol
Surface area47590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.584, 73.886, 109.416
Angle α, β, γ (deg.)90.000, 100.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HIV-1 reverse transcriptase, p66 subunit / Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 subunit, UNP residues 600-1154 / Mutation: C280S, K172A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: Bh10 Isolate / Gene: gag-pol / Plasmid: pCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 reverse transcriptase, p51 subunit


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 subunit, UNP residues 600-1027 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: Bh10 Isolate / Gene: gag-pol / Plasmid: pCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-1RE / 4-({4-methoxy-6-[2-(morpholin-4-yl)ethoxy]-1,3,5-triazin-2-yl}amino)-2-(3-methylbutoxy)benzonitrile


Mass: 442.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N6O4

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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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17.5% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, and 50 mM citric acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2012 / Details: Monochromator
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.89→48.845 Å / Num. all: 28695 / Num. obs: 28706 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 81.02 Å2 / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Χ2: 4.02 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.953.50.4714280.7431100
2.95-33.40.4414340.7781100
3-3.063.30.38314240.865199.9
3.06-3.123.50.35814121.03199.9
3.12-3.193.50.31114381.0931100
3.19-3.273.40.29114031.3571100
3.27-3.353.30.24514311.5181100
3.35-3.443.50.24914251.949199.9
3.44-3.543.50.23214452.4671100
3.54-3.653.50.21514082.7211100
3.65-3.783.30.20614313.4281100
3.78-3.943.50.20714474.2921100
3.94-4.113.50.20114235.3971100
4.11-4.333.40.19214246.005199.9
4.33-4.63.50.19814476.821100
4.6-4.963.40.19214376.768199.9
4.96-5.463.40.18314356.621100
5.46-6.243.40.18314495.9181100
6.24-7.863.40.18314557.161100
7.86-503.30.176151013.3411100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 2ZD1

2zd1


Resolution: 2.89→48.845 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7299 / SU ML: 0.44 / σ(F): 1.35 / σ(I): 1.35 / Phase error: 33.19 / Stereochemistry target values: Maximum Likelihood (ML)
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 1999 6.97 %Random
Rwork0.2457 ---
all0.2487 28695 --
obs0.2457 28695 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.89 Å2 / Biso mean: 58.5786 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.89→48.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7918 0 32 0 7950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038168
X-RAY DIFFRACTIONf_angle_d0.78811098
X-RAY DIFFRACTIONf_chiral_restr0.0591199
X-RAY DIFFRACTIONf_plane_restr0.0031394
X-RAY DIFFRACTIONf_dihedral_angle_d14.4993110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.8898-2.9620.37431290.323417381867173891
2.962-3.04210.38891420.3009188120231881100
3.0421-3.13160.35241420.2875190720491907100
3.1316-3.23270.34091440.2786192220661922100
3.2327-3.34820.35751420.2777190220441902100
3.3482-3.48220.32751430.2672190020431900100
3.4822-3.64060.34941420.2571190020421900100
3.6406-3.83250.29391440.2479192020641920100
3.8325-4.07250.26871450.2292193020751930100
4.0725-4.38680.26161430.2268192020631920100
4.3868-4.82790.2831430.2238190520481905100
4.8279-5.52560.26871450.2269193720821937100
5.5256-6.95850.27721460.2715194220881942100
6.9585-48.85240.25891490.2307199221411992100

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