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- PDB-7so1: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7so1
TitleCrystal Structure of HIV-1 Reverse Transcriptase 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 p66
  • 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
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.727 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 28, 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,5393
Polymers114,0292
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 area5130 Å2
ΔGint-29 kcal/mol
Surface area46160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.030, 73.400, 108.525
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Reverse transcriptase p66


Mass: 63989.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
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: 2.69→50 Å / Num. obs: 33088 / % possible obs: 85.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 59.84 Å2 / Rmerge(I) obs: 0.122 / Χ2: 7.162 / Net I/σ(I): 14.9 / Num. measured all: 121878
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.69-2.742.60.3334821.563125.7
2.74-2.83.50.35519211.557199.8
2.8-2.863.80.32219431.943199.9
2.86-2.933.80.27819072.2371100
2.93-33.80.27219072.71100
3-3.083.80.24619303.0091100
3.08-3.173.80.21619313.6771100
3.17-3.283.80.19219214.5991100
3.28-3.393.80.17119275.7671100
3.39-3.533.80.16119096.9441100
3.53-3.693.80.1519409.029199.8
3.69-3.883.80.14192711.16199.9
3.88-4.133.70.124191410.701199.7
4.13-4.453.70.113192812.803199.3
4.45-4.893.60.107192311.972198.7
4.89-5.63.60.102192411.779199.4
5.6-7.053.60.091194111.213199.5
7.05-503.30.074181313.296189.4

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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: 2.727→38.037 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1654 5 %
Rwork0.2167 31425 -
obs0.2191 33079 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.28 Å2 / Biso mean: 70 Å2 / Biso min: 21.07 Å2
Refinement stepCycle: final / Resolution: 2.727→38.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7828 0 38 0 7866
Biso mean--68.31 --
Num. residues----961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038083
X-RAY DIFFRACTIONf_angle_d0.66710998
X-RAY DIFFRACTIONf_chiral_restr0.0251193
X-RAY DIFFRACTIONf_plane_restr0.0031385
X-RAY DIFFRACTIONf_dihedral_angle_d12.9423043
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.727-2.8070.35821220.2715232188
2.807-2.89750.33631400.25452653100
2.8975-3.0010.36051390.26242641100
3.001-3.12110.31231400.25112661100
3.1211-3.26310.28911390.24282643100
3.2631-3.43510.28741410.22882671100
3.4351-3.65010.27991380.23212634100
3.6501-3.93170.25951400.20812656100
3.9317-4.32680.21681400.1941265899
4.3268-4.95180.23791400.1923266299
4.9518-6.23430.24251410.21542676100
6.2343-38.0370.25611340.2045254992

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