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- PDB-6dtx: Wildtype HIV-1 Reverse Transcriptase in complex with JLJ 578 -

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Basic information

Entry
Database: PDB / ID: 6dtx
TitleWildtype HIV-1 Reverse Transcriptase in complex with JLJ 578
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsHYDROLASE / TRANSFERASE/INHIBITOR / HIV-1 / reverse transcriptase / inhibitor / TRANSFERASE-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 / 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 / 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-H9Y / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.327 Å
AuthorsSasaki, T. / Gannam, Z.T.K. / Anderson, K.S. / Jorgensen, W.L. / Lee, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM049551 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase.
Authors: Sasaki, T. / Gannam, Z.T.K. / Kudalkar, S.N. / Frey, K.M. / Lee, W.G. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.S.
History
DepositionJun 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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)114,5454
Polymers114,0292
Non-polymers5162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-23 kcal/mol
Surface area47710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.166, 69.289, 104.625
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K175A, K174A, Y181C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold
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 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P03366
#3: Chemical ChemComp-H9Y / 8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-6-fluoroindolizine-2-carbonitrile


Mass: 424.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, ammonium sulfate, magnesium sulfate, spermine, MES (pH 6), rilpivirine.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 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: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.327→50 Å / Num. obs: 21940 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rsym value: 0.136 / Net I/σ(I): 22.2
Reflection shellResolution: 3.327→3.41 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1056 / Rsym value: 0.542 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
Cootmodel building
PHASERphasing
HKL-2000data scaling
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mfb

4mfb


Resolution: 3.327→42.596 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.28
RfactorNum. reflection% reflection
Rfree0.2369 1097 5 %
Rwork0.1964 --
obs0.1985 21928 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.327→42.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7853 0 37 0 7890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028105
X-RAY DIFFRACTIONf_angle_d0.45411014
X-RAY DIFFRACTIONf_dihedral_angle_d8.9424881
X-RAY DIFFRACTIONf_chiral_restr0.0411190
X-RAY DIFFRACTIONf_plane_restr0.0041384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3269-3.47830.343950.26051820X-RAY DIFFRACTION68
3.4783-3.66160.29441410.23092661X-RAY DIFFRACTION100
3.6616-3.89080.27291430.21112711X-RAY DIFFRACTION100
3.8908-4.1910.2161420.19062696X-RAY DIFFRACTION100
4.191-4.61230.24761420.17042705X-RAY DIFFRACTION100
4.6123-5.27870.21061430.16932721X-RAY DIFFRACTION100
5.2787-6.64650.27191430.22542724X-RAY DIFFRACTION100
6.6465-42.59990.2091480.19092793X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0251-1.13050.715.1536-1.50134.0422-0.8486-1.3-0.40730.87130.484-0.0074-0.610.48130.25410.85930.1752-0.04321.03440.04670.6555294.3755-1.491540.0428
23.32033.20811.86833.17050.15772.1771-0.6733-0.7920.0824-0.8038-0.1308-0.2253-0.19980.20090.62120.87880.350.13451.1167-0.01911.0017278.167-9.949435.0536
35.05141.48610.67643.28690.76083.4543-0.3295-0.3648-0.7170.44170.29-0.30090.76070.7134-0.03390.76750.3090.08480.79720.04540.772286.0186-13.067126.5967
43.73790.9576-1.08010.1214-0.68931.75410.0387-0.8339-0.66170.0873-0.00210.09820.49110.1923-0.07131.39580.0780.28320.80970.19471.1397255.1817-21.503537.2683
52.4058-1.0681-2.43812.7548-0.47544.6568-0.1294-1.16330.24740.76890.35640.0003-0.65290.2258-0.18691.0461-0.08560.13090.66430.06240.9799245.1743-10.397428.7553
64.7467-1.1796-3.29111.90490.69462.6906-0.0924-0.13730.2746-0.13620.1710.0160.2891-0.3737-0.06430.7547-0.1048-0.03421.02910.04140.979226.1667-2.056532.9173
78.03071.4705-0.40478.652-1.15637.17990.10270.73120.7516-0.9491-0.74010.36920.5558-0.37710.55780.63960.03020.14470.7428-0.02761.0477220.70793.378337.2359
84.0821-0.4652-0.08588.02710.43334-0.2385-0.16920.32580.43290.32010.0881-0.0960.2043-0.06530.5808-0.0367-0.04360.61210.02740.4331266.7787.063613.1006
92.27920.4205-1.01440.9103-0.51881.38230.250.33970.6730.01790.17290.3146-0.3861-0.3877-0.45930.87580.0339-0.04090.78150.16420.8777244.230719.432210.4275
106.72121.0335-2.27349.31090.14793.1814-0.14040.2778-0.34510.67150.4420.5988-0.2164-0.8974-0.26340.88130.04510.02230.70790.0890.5455242.984610.443415.957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 347 )
5X-RAY DIFFRACTION5chain 'A' and (resid 348 through 382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 487 )
7X-RAY DIFFRACTION7chain 'A' and (resid 488 through 548 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 91 )
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 342 )
10X-RAY DIFFRACTION10chain 'B' and (resid 343 through 428 )

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