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- PDB-7so2: Crystal Structure of HIV-1 Reverse Transcriptase Y181C Variant in... -

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Basic information

Entry
Database: PDB / ID: 7so2
TitleCrystal Structure of HIV-1 Reverse Transcriptase Y181C Variant in Complex with (E)-4-((4-((4-(2-cyanovinyl)-2,6-dimethylphenyl)amino)-6-(3-morpholinopropoxy)-1,3,5-triazin-2-yl)amino)benzonitrile (JLJ564)
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
Keywordshydrolase / transferase/viral protein / POLYMERASE / TRANSFERASE / RNASEH / transferase-viral protein 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 / viral penetration into host nucleus / host multivesicular body / 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 / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal 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. / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-9W3 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 Å
AuthorsFrey, K.M. / Anderson, K.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucleoside Inhibitors and Their Interactions With HIV-1 Reverse Transcriptase.
Authors: Frey, K.M. / Bertoletti, N. / Chan, A.H. / Ippolito, J.A. / Bollini, M. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.S.
History
DepositionOct 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4793
Polymers113,9692
Non-polymers5111
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-28 kcal/mol
Surface area46150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.105, 73.101, 107.820
Angle α, β, γ (deg.)90.000, 99.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 63929.207 Da / Num. of mol.: 1 / Mutation: Y181C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein p51 RT


Mass: 50039.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03366
#3: Chemical ChemComp-9W3 / 4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylanilino}-6-[3-(morpholin-4-yl)propoxy]-1,3,5-triazin-2-yl)amino]benzonitrile


Mass: 510.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N8O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, and 50 mM citric acid, pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.089→50 Å / Num. obs: 22651 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 97.06 Å2 / Rmerge(I) obs: 0.087 / Χ2: 3.036 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.089-3.153.40.51511300.879198.9
3.15-3.213.50.47310840.872199.4
3.21-3.273.60.3811410.992199.9
3.27-3.343.70.31911411.0721100
3.34-3.413.70.27111211.2011100
3.41-3.493.70.38711485.2611100
3.49-3.583.70.19611101.4451100
3.58-3.683.70.24711414.5371100
3.68-3.783.80.16111092.1051100
3.78-3.913.70.21911266.454199.9
3.91-4.043.70.1211582.8681100
4.04-4.213.70.10711092.846199.6
4.21-4.43.70.0911372.936199.8
4.4-4.633.70.08511263.393199.8
4.63-4.923.70.07711403.231199.8
4.92-5.33.70.07511273.346199.7
5.3-5.833.70.07711473.4461100
5.83-6.673.60.06511512.812199.9
6.67-8.43.50.05311503.789199.6
8.4-503.50.05111556.84196.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZD1

2zd1


Resolution: 3.089→42.88 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2817 1132 5 %
Rwork0.2276 21502 -
obs0.2304 22634 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.11 Å2 / Biso mean: 98.19 Å2 / Biso min: 38.8 Å2
Refinement stepCycle: final / Resolution: 3.089→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7599 0 38 0 7637
Biso mean--100.85 --
Num. residues----940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037842
X-RAY DIFFRACTIONf_angle_d0.64910671
X-RAY DIFFRACTIONf_chiral_restr0.0251167
X-RAY DIFFRACTIONf_plane_restr0.0031344
X-RAY DIFFRACTIONf_dihedral_angle_d12.8412947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0891-3.22970.37471300.2877247192
3.2297-3.39990.32161430.26562714100
3.3999-3.61280.33111410.25862679100
3.6128-3.89160.30761430.24122717100
3.8916-4.28290.29061430.23262714100
4.2829-4.90180.27371440.20992729100
4.9018-6.17290.29731430.24562722100
6.1729-42.880.23981450.2012275698

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