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- PDB-6oe3: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 6oe3
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-7-fluoro-2-naphthonitrile (JLJ635), a Non-nucleoside Inhibitor
Components(HIV-1 REVERSE TRANSCRIPTASE, ...) x 2
KeywordsTRANSFERASE / NNRTIs / HIV-1 / drug design
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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-M9A / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBertoletti, N. / Kudalkar, S.N. / Anderson, K.S. / Cisneros Trigo, J.A. / Jorgensen, W.L.
Funding support United States, 3items
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)AI141572 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI044616 United States
CitationJournal: Antiviral Res. / Year: 2019
Title: Structural and pharmacological evaluation of a novel non-nucleoside reverse transcriptase inhibitor as a promising long acting nanoformulation for treating HIV.
Authors: Kudalkar, S.N. / Ullah, I. / Bertoletti, N. / Mandl, H.K. / Cisneros, J.A. / Beloor, J. / Chan, A.H. / Quijano, E. / Saltzman, W.M. / Jorgensen, W.L. / Kumar, P. / Anderson, K.S.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: 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: HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5665
Polymers114,0292
Non-polymers5383
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-43 kcal/mol
Surface area45540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.311, 69.572, 104.830
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HIV-1 REVERSE TRANSCRIPTASE, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT / p66 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S, C258Q
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) / Variant (production host): GOLD
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT


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) / Variant (production host): GOLD / References: UniProt: P03366

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Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-M9A / 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-7-fluoronaphthalene-2-carbonitrile


Mass: 417.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16FN3O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.45 Å3/Da / Density % sol: 64.4 % / Description: thin plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES pH 6.0, 18% 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 34181 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.996 / Rsym value: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5280 / CC1/2: 0.63 / Rsym value: 1.098 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW3

5tw3


Resolution: 2.9→43.171 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.4
RfactorNum. reflection% reflection
Rfree0.2729 1701 4.99 %
Rwork0.228 --
obs0.2303 34093 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7550 0 37 13 7600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067794
X-RAY DIFFRACTIONf_angle_d0.82110651
X-RAY DIFFRACTIONf_dihedral_angle_d14.84646
X-RAY DIFFRACTIONf_chiral_restr0.0511182
X-RAY DIFFRACTIONf_plane_restr0.0071383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8983-2.98360.47591280.48382451X-RAY DIFFRACTION90
2.9836-3.07990.43181440.34832718X-RAY DIFFRACTION99
3.0799-3.18990.38431430.29472740X-RAY DIFFRACTION100
3.1899-3.31760.34371430.30342718X-RAY DIFFRACTION99
3.3176-3.46850.34541430.29562729X-RAY DIFFRACTION99
3.4685-3.65130.33341420.28872686X-RAY DIFFRACTION98
3.6513-3.87990.36921300.2992539X-RAY DIFFRACTION92
3.8799-4.17930.29071420.22352700X-RAY DIFFRACTION98
4.1793-4.59940.21291440.17662730X-RAY DIFFRACTION99
4.5994-5.2640.20621460.16932775X-RAY DIFFRACTION100
5.264-6.62820.26271460.20892765X-RAY DIFFRACTION99
6.6282-43.17540.21141500.17752841X-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)
13.47470.58850.79423.9075-0.72425.495-0.2527-0.53290.030.4732-0.16710.0853-0.44160.0530.41690.74770.1069-0.12620.8257-0.12020.7099458.228218.1103237.9692
23.8017-1.07770.44598.8879-0.93716.6405-0.4514-0.9889-0.05740.83890.0268-0.9236-0.12280.15330.44280.75340.1585-0.13011.2238-0.13350.8231466.694610.4059243.0965
34.1396-5.12114.86846.3773-6.30817.68450.2261-0.6889-0.80740.2628-0.13120.1322-0.0367-0.6704-0.13790.86840.1018-0.27742.20160.66971.3213459.8844-1.2501250.5145
43.52840.77620.14721.94330.11930.415-0.1339-0.5015-0.59050.16330.0036-0.18650.29310.22070.13250.73540.15150.05440.66070.11130.6339444.947-0.0226232.9035
54.43953.00245.21142.45123.38366.16310.6534-0.91640.2764-0.6289-0.12290.1015-0.50640.024-0.60391.4347-0.186-0.07821.3952-0.05531.3449422.424810.1179255.0648
63.44871.4809-0.51471.3221-1.62642.9224-0.2622-0.2434-0.47810.25860.04160.02950.2765-0.25740.17730.86640.03380.26750.55670.06740.9095415.7127-3.3155232.6081
74.7754-1.7627-2.99622.33762.2353.8043-0.1024-0.05110.0421-0.13070.0546-0.15010.2221-0.18720.03910.5578-0.04030.04560.58210.07580.8193391.175816.435237.5244
83.2806-1.13570.11455.6761-0.16594.8905-0.33830.06210.32490.37030.1084-0.1406-0.15780.0160.22230.49820.0186-0.04950.53010.06280.5293435.162622.2631215.2213
94.151-1.67671.24082.7454-1.27572.1919-0.29850.34430.32960.46590.1387-0.0402-0.4678-0.00640.1870.6059-0.02710.04510.4970.06060.5318434.275926.0042211.1202
108.7812-1.05611.03013.57131.09176.76410.04510.7944-0.1461-0.05360.03230.32090.0976-0.4021-0.07520.5603-0.058-0.00080.70130.15630.6224424.074137.1137196.2255
114.6290.8811-1.64952.2292-0.36143.46830.06390.5891.0704-0.64030.17220.1269-0.4977-0.4825-0.31070.7940.07430.19720.97360.3491.0097389.097637.3165224.5681
126.08920.9903-1.96930.9148-1.18471.59390.33970.12731.31990.06320.09280.2181-0.4075-0.4557-0.44960.77650.077-0.03460.71210.14220.9519397.641536.4234222.171
135.3553-2.367-1.68555.8365-3.90445.0452-1.29572.1657-1.518-1.99330.22192.24250.2656-1.28220.57850.8436-0.2233-0.34340.9665-0.12871.1268407.24715.9363211.5602
145.38280.5712-1.59137.2885-0.93944.34570.0276-0.0889-0.39150.7515-0.07590.0116-0.0629-0.12430.10750.67320.02510.05620.51970.0290.5581413.689625.1112218.9668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:29)
2X-RAY DIFFRACTION2(chain A and resid 30:63)
3X-RAY DIFFRACTION3(chain A and resid 64:72)
4X-RAY DIFFRACTION4(chain A and resid 73:282)
5X-RAY DIFFRACTION5(chain A and resid 283:290)
6X-RAY DIFFRACTION6(chain A and resid 291:392)
7X-RAY DIFFRACTION7(chain A and resid 393:552)
8X-RAY DIFFRACTION8(chain B and resid 5:95)
9X-RAY DIFFRACTION9(chain B and resid 96:159)
10X-RAY DIFFRACTION10(chain B and resid 160:237)
11X-RAY DIFFRACTION11(chain B and resid 238:281)
12X-RAY DIFFRACTION12(chain B and resid 282:356)
13X-RAY DIFFRACTION13(chain B and resid 357:369)
14X-RAY DIFFRACTION14(chain B and resid 370:428)

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