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- PDB-3isn: Crystal structure of HIV-1 RT bound to A 6-vinylpyrimidine inhibitor -

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Basic information

Entry
Database: PDB / ID: 3isn
TitleCrystal structure of HIV-1 RT bound to A 6-vinylpyrimidine inhibitor
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / HYDROLASE / HIV-1 / inhibitor / RT
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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-EDM / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEnnifar, E. / Freisz, S. / Bec, G. / Dumas, P. / Botta, M. / Radi, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Crystal Structure of HIV-1 Reverse Transcriptase Bound to a Non-Nucleoside Inhibitor with a Novel Mechanism of Action
Authors: Freisz, S. / Bec, G. / Radi, M. / Wolff, P. / Crespan, E. / Angeli, L. / Dumas, P. / Maga, G. / Botta, M. / Ennifar, E.
History
DepositionAug 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 28, 2025Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6713
Polymers114,4432
Non-polymers2271
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-30 kcal/mol
Surface area45430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.121, 72.182, 93.516
Angle α, β, γ (deg.)90.00, 108.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-586-

HOH

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Components

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


Mass: 64516.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Strain: type 1 BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein p51 RT


Mass: 49927.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Strain: type 1 BH10 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#3: Chemical ChemComp-EDM / 6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine


Mass: 227.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsE465Q IS MUTAGENESIS ACCORDING TO REFERENCE 9 OF DATABASE UNIPROTKB/SWISS-PROT P03366 (POL_HV1B1).

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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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Bis-Tris , 25% PEG 3350, 200mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.2824 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2008 / Details: crystal
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 49675 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 52.08 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.062 / Net I/σ(I): 26.49
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.53 / Num. unique all: 40894 / Rsym value: 0.737 / % possible all: 67.4

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.4_57)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1DLO

1dlo


Resolution: 2.5→49.102 Å / FOM work R set: 0.704 / SU ML: 0.41 / σ(F): 0 / σ(I): 0 / Phase error: 35.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2805 1998 4.55 %
Rwork0.2209 --
obs0.2236 43911 88.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 154.84 Å2 / Biso mean: 63.51 Å2 / Biso min: 25.42 Å2
Baniso -1Baniso -2Baniso -3
1--6.292 Å20 Å26.84 Å2
2--8.35 Å20 Å2
3---1.627 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7941 0 15 204 8160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018173
X-RAY DIFFRACTIONf_angle_d1.35311109
X-RAY DIFFRACTIONf_dihedral_angle_d19.7563072
X-RAY DIFFRACTIONf_chiral_restr0.0851205
X-RAY DIFFRACTIONf_plane_restr0.0071399
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4993-2.56180.44681530.4562320595
2.5618-2.6310.38281580.30913319100
2.631-2.70840.288320.323766820
2.7084-2.79590.37671600.29263359100
2.7959-2.89580.41771620.26183381100
2.8958-3.01170.30361590.23653348100
3.0117-3.14870.31351590.23493350100
3.1487-3.31470.32541590.2412332399
3.3147-3.52230.28331130.2455235270
3.5223-3.79420.26851230.2144260077
3.7942-4.17590.27441310.1912273781
4.1759-4.77970.21261610.17073380100
4.7797-6.02020.23431630.18523412100
6.0202-49.11170.23971650.18783479100

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