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

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Basic information

Entry
Database: PDB / ID: 5vqx
TitleCrystal Structure of HIV-1 Reverse Transcriptase (Y181C) Variant in Complex with 2-chloro-N-(6-cyano-3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-4-methylnaphthalen-1-yl)-N-methylacetamide (JLJ686), 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 / 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 / DNA integration / host multivesicular body / 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 / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / 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 / 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. / 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-9HY / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsChan, A.H. / 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 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)114,6455
Polymers113,9692
Non-polymers6773
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: RT is known to function as a heterdimer of p66 and p51
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-59 kcal/mol
Surface area46650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.300, 73.530, 108.670
Angle α, β, γ (deg.)90.000, 99.300, 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 / Fragment: p66 / 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 / Fragment: p51 / 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-9HY / N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)-N-methylacetamide


Mass: 484.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24N4O5
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM imidazole pH 6.8, 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 9, 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: 2.4→43.202 Å / Num. obs: 49576 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.708 % / Biso Wilson estimate: 48.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.057 / Χ2: 1.059 / Net I/σ(I): 17.15 / Num. measured all: 183830 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.463.7920.5112.6336760.8220.59599.9
2.46-2.533.7880.4083.2635600.8920.476100
2.53-2.63.80.3194.1634250.9230.37299.9
2.6-2.683.7430.2735.0933770.9420.31999.8
2.68-2.773.7770.2066.4832510.9650.24199.8
2.77-2.873.7830.1538.3431640.9820.17999.8
2.87-2.983.7830.11810.9430380.9890.13799.9
2.98-3.13.7830.09612.9729220.9920.112100
3.1-3.243.750.07516.5928000.9940.08899.9
3.24-3.393.7230.05720.2727000.9970.067100
3.39-3.583.6260.04824.3125650.9970.05699.4
3.58-3.793.5820.03927.4423960.9980.04699.5
3.79-4.063.5440.03531.5823070.9980.04299.1
4.06-4.383.5970.03233.5921040.9980.038100
4.38-4.83.5940.03135.2319560.9980.03699.8
4.8-5.373.5730.02935.7117880.9980.03599.8
5.37-6.23.6040.02935.415790.9980.035100
6.2-7.593.5980.02537.3713420.9990.02999.6
7.59-10.733.6620.0241.410510.9990.02399.6
10.73-43.2023.4660.01841.135750.9990.02295.7

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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: 5VQQ

5vqq


Resolution: 2.4→43.202 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 2000 4.03 %Random selection
Rwork0.2258 ---
obs0.2273 49571 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.97 Å2 / Biso mean: 58.2888 Å2 / Biso min: 23.27 Å2
Refinement stepCycle: final / Resolution: 2.4→43.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 46 151 7933
Biso mean--55.48 48.34 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027994
X-RAY DIFFRACTIONf_angle_d0.48810876
X-RAY DIFFRACTIONf_chiral_restr0.0421178
X-RAY DIFFRACTIONf_plane_restr0.0031367
X-RAY DIFFRACTIONf_dihedral_angle_d9.8884789
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 (%)
2.4-2.460.35961430.301733913534100
2.46-2.52650.31241420.291533953537100
2.5265-2.60090.34881420.277133543496100
2.6009-2.68480.31221410.274833863527100
2.6848-2.78070.35621420.267633863528100
2.7807-2.8920.33051420.268533673509100
2.892-3.02360.33791420.274733743516100
3.0236-3.1830.32851440.267234293573100
3.183-3.38240.27491420.253433683510100
3.3824-3.64340.28181430.245333953538100
3.6434-4.00980.23951420.2153373351599
4.0098-4.58950.22371430.1934193562100
4.5895-5.78010.23261440.194934283572100
5.7801-43.20920.19571480.18153506365499

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