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- PDB-5vqr: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5vqr
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with N-(6-cyano-3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-4-methylnaphthalen-1-yl)-N-methylacrylamide (JLJ684), a Non-nucleoside Inhibitor
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/HYDROLASE/INHIBITOR / Polymerase / reverse transcriptase / non-nucleoside inhibitor / TRANSFERASE-HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA stem-loop binding / 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 / viral translational frameshifting / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / 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. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain 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-9KG / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 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 1.3Dec 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)114,6214
Polymers114,0292
Non-polymers5932
Water72140
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 area5380 Å2
ΔGint-44 kcal/mol
Surface area46500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.430, 73.730, 108.350
Angle α, β, γ (deg.)90.000, 99.690, 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: 63989.238 Da / Num. of mol.: 1 / Mutation: C280S, K172A, K173A
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-9KG / N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)-N-methylprop-2-enamide


Mass: 496.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N4O5
#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.: 40 / 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: 56.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM imidazole pH 6.8, 14% 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: Dec 13, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→43.233 Å / Num. obs: 41097 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.754 % / Biso Wilson estimate: 59.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.054 / Χ2: 1.016 / Net I/σ(I): 18.93 / Num. measured all: 154293 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.623.730.6152.3229960.7290.71899.5
2.62-2.693.7780.5032.8729530.8270.58699.2
2.69-2.773.8250.3793.9128570.8940.4499.3
2.77-2.853.8240.2775.1328070.9380.32299.3
2.85-2.943.820.2066.8726950.9650.2499.6
2.94-3.053.8140.1628.5326260.9780.18899.2
3.05-3.163.810.12111.2425020.9870.14199.5
3.16-3.293.8030.08614.6624340.9920.199.4
3.29-3.443.8030.06418.623390.9960.07499.3
3.44-3.613.7890.0522.9722490.9970.05899.6
3.61-3.83.7670.0427.2621070.9980.04699.3
3.8-4.033.7240.0343220300.9980.0499.7
4.03-4.313.7120.0335.2619020.9980.03599.2
4.31-4.663.7210.02837.5617500.9990.03299.3
4.66-5.13.6470.02838.9316220.9980.03398.7
5.1-5.73.6020.02838.5614950.9980.03399.3
5.7-6.583.6410.02839.3112930.9980.03399.1
6.58-8.063.610.02543.0911140.9990.02998.5
8.06-11.43.6160.02347.378550.9990.02698.2
11.4-43.2333.3820.02246.634710.9990.02692

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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: 2.55→43.233 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.89
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 2000 4.87 %Random selection
Rwork0.2261 ---
obs0.2273 41085 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.84 Å2 / Biso mean: 71.58 Å2 / Biso min: 26.32 Å2
Refinement stepCycle: final / Resolution: 2.55→43.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 42 40 7802
Biso mean--73.27 54.43 -
Num. residues----947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027975
X-RAY DIFFRACTIONf_angle_d0.49410855
X-RAY DIFFRACTIONf_chiral_restr0.0421178
X-RAY DIFFRACTIONf_plane_restr0.0031366
X-RAY DIFFRACTIONf_dihedral_angle_d9.784772
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 (%)
2.55-2.61380.37941410.32462757289899
2.6138-2.68440.3041410.29632759290099
2.6844-2.76340.36911420.27892775291799
2.7634-2.85260.2851430.2742795293899
2.8526-2.95450.32031420.276727732915100
2.9545-3.07280.26691430.27882810295399
3.0728-3.21260.28841420.27182766290899
3.2126-3.38190.29111430.25862775291899
3.3819-3.59370.30771430.25572812295599
3.5937-3.8710.25021440.23182807295199
3.871-4.26030.25781420.200127922934100
4.2603-4.8760.23031440.19722797294199
4.876-6.14050.21371440.20742817296199
6.1405-43.23940.17961460.18132850299698

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