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- PDB-5vqw: Crystal Structure of HIV-1 Reverse Transcriptase (Y181C) Variant ... -

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Basic information

Entry
Database: PDB / ID: 5vqw
TitleCrystal Structure of HIV-1 Reverse Transcriptase (Y181C) Variant in Complex with N-(6-cyano-3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-4-methylnaphthalen-1-yl)acrylamide (JLJ685), a Non-nucleoside Inhibitor
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/HYDROLASE/INHIBITOR / Polymerase / reverse transcriptase / HIV / non-nucleoside inhibitor / TRANSFERASE-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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / 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 / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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-9KD / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsChan, A.H. / Kudalkar, S.N. / Anderson, K.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049551 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI044616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM032136 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI122864 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography.
Authors: Chan, A.H. / Lee, W.G. / Spasov, K.A. / Cisneros, J.A. / Kudalkar, S.N. / Petrova, Z.O. / Buckingham, A.B. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionMay 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,5474
Polymers113,9692
Non-polymers5792
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: RT is known to function as a heterodimer of p66 and p51 subunits
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-45 kcal/mol
Surface area46400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.060, 73.820, 108.200
Angle α, β, γ (deg.)90.000, 99.610, 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: C280S, K172A, K173A, 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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366
#3: Chemical ChemComp-9KD / N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)prop-2-enamide


Mass: 482.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22N4O5
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM HEPES pH 7.0, 16% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→43.193 Å / Num. obs: 43755 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.756 % / Biso Wilson estimate: 58.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.043 / Χ2: 1.003 / Net I/σ(I): 23.37 / Num. measured all: 164348 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.563.8080.5492.4632210.8050.6499.9
2.56-2.643.8080.4163.2331660.8680.48499.7
2.64-2.713.7830.3264.230230.9120.3899.9
2.71-2.83.8080.2475.4129860.9520.287100
2.8-2.893.8150.1817.3728560.9720.21199.7
2.89-2.993.8050.1319.8827810.9860.15399.9
2.99-3.13.7950.10512.4327020.990.122100
3.1-3.233.8020.07616.925760.9940.08999.8
3.23-3.373.7910.05322.4224890.9970.062100
3.37-3.543.7510.04128.0323780.9980.04899.6
3.54-3.733.7480.03334.2822570.9990.03899.5
3.73-3.953.7120.02739.6721310.9990.03199.6
3.95-4.233.7330.02344.5720060.9990.02799.8
4.23-4.563.6970.02248.3218880.9990.02599.7
4.56-53.6710.02149.9617320.9990.02599.8
5-5.593.620.0225015700.9990.02699.7
5.59-6.453.6630.02250.0613960.9990.02699.7
6.45-7.913.6630.0254.9911740.9990.02399.5
7.91-11.183.6660.01760.819300.9990.0299.5
11.18-43.1933.320.01758.974930.9990.0292.3

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Processing

Software
NameVersionClassification
XSCALENov 1, 2016data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSNov 1, 2016data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5TER

5ter


Resolution: 2.5→43.193 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 2000 4.57 %Random Selection
Rwork0.2326 ---
obs0.2337 43748 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.2 Å2 / Biso mean: 72.9922 Å2 / Biso min: 28.61 Å2
Refinement stepCycle: final / Resolution: 2.5→43.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 41 61 7832
Biso mean--80.18 56.29 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027983
X-RAY DIFFRACTIONf_angle_d0.49310860
X-RAY DIFFRACTIONf_chiral_restr0.0421178
X-RAY DIFFRACTIONf_plane_restr0.0031366
X-RAY DIFFRACTIONf_dihedral_angle_d9.7084783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56250.36741420.315229703112100
2.5625-2.63180.36351430.295529873130100
2.6318-2.70930.33811420.29229543096100
2.7093-2.79670.31891430.299529723115100
2.7967-2.89660.32541400.278429383078100
2.8966-3.01260.29071420.276429623104100
3.0126-3.14960.3691430.280629903133100
3.1496-3.31560.30161440.27430003144100
3.3156-3.52330.28151420.250829713113100
3.5233-3.79520.24941410.239229453086100
3.7952-4.17680.23011440.21329943138100
4.1768-4.78050.19981430.199629933136100
4.7805-6.02040.2511450.211930233168100
6.0204-43.19960.21121460.19523049319599

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