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- PDB-2b6a: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -

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Basic information

Entry
Database: PDB / ID: 2b6a
TitleCrystal structure of HIV-1 reverse transcriptase (RT) in complex with THR-50
Components
  • Reverse transcriptase p51 subunit
  • Reverse transcriptase p66 subunit
KeywordsTRANSFERASE / AIDS / HIV / DRUG DESIGN / REVERSE TRANSCRIPTASE / RT / PROTEIN-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-T50 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMorningstar, M.L. / Roth, T. / Smith, M.K. / Zajac, M. / Watson, K. / Buckheit, R.W. / Das, K. / Zhang, W. / Arnold, E. / Michejda, C.J.
Citation
Journal: TO BE PUBLISHED
Title: Crystal structure of HIV-1 reverse transcriptase (RT) in complex with THR-50
Authors: Morningstar, M.L. / Roth, T. / Smith, M.K. / Zajac, M. / Watson, K. / Buckheit, R.W. / Das, K. / Zhang, W. / Arnold, E. / Michejda, C.J.
#1: Journal: J.Med.Chem. / Year: 1997
Title: Synthesis and biological activity of novel nonnucleoside inhibitors of HIV-1 reverse transcriptase. 2-Aryl-substituted benzimidazoles.
Authors: Roth, T. / Morningstar, M.L. / Boyer, P.L. / Hughes, S.H. / Buckheit, R.W. / Michejda, C.J.
History
DepositionSep 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase p66 subunit
B: Reverse transcriptase p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1533
Polymers114,7832
Non-polymers3701
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-18 kcal/mol
Surface area48750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.706, 70.168, 106.630
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Reverse transcriptase p66 subunit / HIV-1 RT


Mass: 64500.965 Da / Num. of mol.: 1 / Fragment: RESIDUES 599-1158 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase p51 subunit / HIV-1 RT


Mass: 50281.762 Da / Num. of mol.: 1 / Fragment: RESIDUES 599-1028 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical ChemComp-T50 / 1-(2,6-DIFLUOROBENZYL)-2-(2,6-DIFLUOROPHENYL)-4-METHYL-1H-BENZIMIDAZOLE


Mass: 370.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14F4N2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.8
Details: PEG8000, AMMINIUM SULPHATE, SODIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 268 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 49714 / % possible obs: 88.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNV

1hnv


Resolution: 2.65→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2317991.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2245 5 %RANDOM
Rwork0.226 ---
all0.233 47290 --
obs-44766 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.123 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 83.972 Å2
Baniso -1Baniso -2Baniso -3
1-8.11 Å20 Å226.45 Å2
2---9.56 Å20 Å2
3---1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 27 0 7921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.437 319 4.9 %
Rwork0.389 6134 -
all-6453 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2t50.topt50.par

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