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- PDB-4ko0: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 4ko0
TitleCRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH an anilinylpyrimidine derivative (JLJ-135)
Components(HIV-1 reverse transcriptase, ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / P51/P66 / HETERO DIMER / NNRTI / NONNUCLEOSIDE INHIBITOR / AIDS / HIV / DNA RECOMBINATION / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSFERASE / HYDROLASE-INHIBITOR COMPLEX / 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 / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / 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-JLJ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDas, K. / Bauman, J.D. / Arnold, E.
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 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 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)114,6557
Polymers114,0292
Non-polymers6275
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-29 kcal/mol
Surface area47750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.209, 73.950, 109.202
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HIV-1 reverse transcriptase, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 reverse transcriptase, p66 subunit / Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT / p51 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: 1B1 / Gene: gag-pol / Plasmid: PRT52A / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 reverse transcriptase, p51 subunit / Reverse transcriptase/ribonuclease H / Exoribonuclease H / p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: 1B1 / Gene: gag-pol / Plasmid: PRT52A / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 / References: UniProt: P03366, RNA-directed DNA polymerase

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Non-polymers , 4 types, 343 molecules

#3: Chemical ChemComp-JLJ / 4-[(4-methoxypyrimidin-2-yl)amino]-2-[(3-methylbut-2-en-1-yl)oxy]benzonitrile


Mass: 310.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 277 K / pH: 6.8
Details: PEG 8000, AMMONIUM SULFATE, MGCL2, IMIDAZOLE , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2006 / Details: MONOCHROMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 91737 / % possible obs: 98.8 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S9E

1s9e


Resolution: 1.95→29.31 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 1862 2.03 %
Rwork0.237 --
obs0.238 91715 98.8 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.01 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4192 Å20 Å2-3.4893 Å2
2---2.3077 Å2-0 Å2
3---3.7269 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7912 0 41 338 8291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098184
X-RAY DIFFRACTIONf_angle_d1.11411123
X-RAY DIFFRACTIONf_dihedral_angle_d14.9623103
X-RAY DIFFRACTIONf_chiral_restr0.0741201
X-RAY DIFFRACTIONf_plane_restr0.0051399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.33061310.32026872X-RAY DIFFRACTION99
2.0027-2.06160.29651450.29926939X-RAY DIFFRACTION99
2.0616-2.12820.35391470.28516893X-RAY DIFFRACTION99
2.1282-2.20420.29951490.27536875X-RAY DIFFRACTION100
2.2042-2.29240.36891190.30456828X-RAY DIFFRACTION97
2.2924-2.39670.28411550.26046936X-RAY DIFFRACTION100
2.3967-2.5230.33611450.25086969X-RAY DIFFRACTION100
2.523-2.6810.28661440.2476944X-RAY DIFFRACTION100
2.681-2.88780.30021580.24426987X-RAY DIFFRACTION100
2.8878-3.17810.28681440.24066969X-RAY DIFFRACTION100
3.1781-3.63730.25391440.22716963X-RAY DIFFRACTION99
3.6373-4.57970.23971460.20056946X-RAY DIFFRACTION99
4.5797-29.31450.26311350.23136732X-RAY DIFFRACTION94

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