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

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Basic information

Entry
Database: PDB / ID: 4lsl
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with (E)-3-(3-(4-chloro-2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)phenyl)acrylonitrile (JLJ476), a non-nucleoside inhibitor
Components
  • HIV-1 reverse transcriptase, p51 subunit
  • HIV-1 reverse transcriptase, p66 subunit
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Polymerase / Transferase / Hydrolase / RnaseH / 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 / 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 / symbiont-mediated suppression of host gene expression / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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-1YQ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsFrey, K.M. / Anderson, K.S.
CitationJournal: Chem.Biol.Drug Des. / Year: 2014
Title: Structure-Based Evaluation of C5 Derivatives in the Catechol Diether Series Targeting HIV-1 Reverse Transcriptase.
Authors: Frey, K.M. / Gray, W.T. / Spasov, K.A. / Bollini, M. / Gallardo-Macias, R. / Jorgensen, W.L. / Anderson, K.S.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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)114,4393
Polymers114,0292
Non-polymers4101
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-23 kcal/mol
Surface area48640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.872, 69.316, 104.341
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HIV-1 reverse transcriptase, p66 subunit


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-1YQ / (2E)-3-(3-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile / (E)-3-(3-bromo-5-(4-chloro-2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)phenyl)acrylonitrile


Mass: 409.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16ClN3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% (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: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2013 / Details: Monochromator
RadiationMonochromator: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 42552 / Num. obs: 42552 / % possible obs: 98.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.8 % / Biso Wilson estimate: 77.02 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.069 / Χ2: 3.093 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.69-2.743.80.42721441.0581100
2.74-2.793.80.39521381.0461100
2.79-2.843.80.31321161.2151100
2.84-2.93.80.25821551.3481100
2.9-2.963.80.21721161.4611100
2.96-3.033.80.19421511.6141100
3.03-3.113.80.1721271.8461100
3.11-3.193.80.14121572.1251100
3.19-3.283.80.1221542.5041100
3.28-3.393.80.11121212.8621100
3.39-3.513.80.09821313.1621100
3.51-3.653.80.08921623.5871100
3.65-3.823.80.08221484.1571100
3.82-4.023.80.07621464.4811100
4.02-4.273.80.06921364.6651100
4.27-4.63.80.06521605.18199.7
4.6-5.063.70.06421565.829199.6
5.06-5.793.70.06421825.8111100
5.79-7.293.60.04721774.1471100
7.29-503.40.0417754.123178.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H4M

4h4m


Resolution: 2.69→34.766 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.7355 / SU ML: 0.39 / σ(F): 1.34 / σ(I): 1.34 / Phase error: 32.37 / Stereochemistry target values: Maximum Likelihood (ML)
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1999 4.7 %Random
Rwork0.2437 ---
all0.2449 42542 --
obs0.2437 42542 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 279.66 Å2 / Biso mean: 91.132 Å2 / Biso min: 28.39 Å2
Refinement stepCycle: LAST / Resolution: 2.69→34.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 29 35 7958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038141
X-RAY DIFFRACTIONf_angle_d0.81811064
X-RAY DIFFRACTIONf_chiral_restr0.0631197
X-RAY DIFFRACTIONf_plane_restr0.0041392
X-RAY DIFFRACTIONf_dihedral_angle_d13.8013091
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 (%)
2.6902-2.75740.35421380.355628012939280196
2.7574-2.83190.39321430.352289130342891100
2.8319-2.91520.38511430.3459292830712928100
2.9152-3.00930.39891450.3397293030752930100
3.0093-3.11680.40611420.3239288530272885100
3.1168-3.24150.31251450.2869291930642919100
3.2415-3.38890.3221440.2893294830922948100
3.3889-3.56740.30991450.2781292530702925100
3.5674-3.79060.29641430.2631291730602917100
3.7906-4.08290.27051470.2419295431012954100
4.0829-4.4930.23361440.2075293230762932100
4.493-5.14140.22181440.2002293230762932100
5.1414-6.47070.25821470.2249297931262979100
6.4707-34.76920.21041290.207926022731260285

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