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- PDB-7kre: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7kre
TitleCrystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-((6-cyanonaphthalen-1-yl)oxy)-3-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenyl sulfurofluoridate (JLJ704)
Components
  • HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
  • HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT
KeywordsTRANSFERASE / Hydrolase/Inhibitor / Polymerase / reverse transcriptase / non-nucleoside inhibitor / 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 / 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 / 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
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 ...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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / 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 / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-X2V / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.728 Å
AuthorsBertoletti, N. / Ippolito, J.A. / Jorgensen, W.L. / Anderson, K.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49551 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155072 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead.
Authors: Ippolito, J.A. / Niu, H. / Bertoletti, N. / Carter, Z.J. / Jin, S. / Spasov, K.A. / Cisneros, J.A. / Valhondo, M. / Cutrona, K.J. / Anderson, K.S. / Jorgensen, W.L.
History
DepositionNov 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 18, 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)114,5263
Polymers114,0292
Non-polymers4971
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-23 kcal/mol
Surface area46320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.573, 69.554, 104.859
Angle α, β, γ (deg.)90.000, 105.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 63989.238 Da / Num. of mol.: 1
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)
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
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) / References: UniProt: P03366
#3: Chemical ChemComp-X2V / 4-[(6-cyanonaphthalen-1-yl)oxy]-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate


Mass: 497.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16FN3O7S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM imidazole pH 6.5, 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: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.728→57.624 Å / Num. obs: 41954 / % possible obs: 99.3 % / Redundancy: 6.421 % / Biso Wilson estimate: 98.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.051 / Χ2: 1.194 / Net I/σ(I): 19.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.728-2.896.3370.9811.4542602680567230.8251.06898.8
2.89-3.096.6420.4963.0242053634663310.9460.53899.8
3.09-3.346.2460.2346.236682593758730.9840.25598.9
3.34-3.666.8180.1212.9337337549754760.9960.12999.6
3.66-4.096.5450.06224.4632416497049530.9980.06799.7
4.09-4.726.2060.0437.4527064438743610.9990.04399.4
4.72-5.786.3330.03545.6823349372536870.9990.03999
5.78-8.166.2950.03151.2718261291629010.9990.03499.5
8.16-57.6245.8450.02559.329639168016490.9990.02798.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW3

5tw3


Resolution: 2.728→57.624 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 2092 4.99 %
Rwork0.2104 39802 -
obs0.2129 41894 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 317.48 Å2 / Biso mean: 126.1265 Å2 / Biso min: 65.36 Å2
Refinement stepCycle: final / Resolution: 2.728→57.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7447 0 35 0 7482
Biso mean--95.93 --
Num. residues----940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.728-2.79110.53251380.5055261498
2.7911-2.86090.43371370.3661261399
2.8609-2.93820.36351380.3181262299
2.9382-3.02470.34071410.2831266999
3.0247-3.12230.28951380.2742640100
3.1223-3.23390.33251370.2718263899
3.2339-3.36340.33541360.2542260798
3.3634-3.51640.28551400.23862653100
3.5164-3.70180.31531410.2283267199
3.7018-3.93360.24971390.21852637100
3.9336-4.23730.26731410.20062674100
4.2373-4.66350.24351400.17422665100
4.6635-5.33790.23821390.1753264699
5.3379-6.72360.27781430.21982708100
6.7236-57.6240.20621440.1837274599
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)
10.5693-0.0859-0.48840.4459-0.22090.3444-0.32090.32570.3217-0.1099-0.13580.23120.08020.3263-0.00320.96790.2177-0.18411.002-0.19450.7554491.8969.802137.922
20.20730.372-0.24990.4056-0.11460.3365-0.2789-1.556-0.5702-0.0872-0.37240.02040.6951.1806-0.01041.03530.4333-0.26012.0688-0.05521.1569499.9722.332141.803
30.04440.0001-0.01170.01570.011-0.02670.4518-0.1857-0.64751.10850.8844-0.66020.1690.51620.0021.00180.0423-0.27262.1247-0.05242.7459491.353-11.923148.638
42.54830.1675-0.11560.60640.64880.6279-0.3638-0.7089-0.5220.13460.13050.04140.44380.26310.12381.0460.3066-0.01020.95420.16610.7378478.049-7.996132
50.0708-0.0288-0.0770.0511-0.02430.12290.4117-0.64840.2711-0.6391-0.6-0.1364-0.63860.09260.00042.07550.075101.8223-0.06441.637454.7822.196153.824
62.90710.82-0.1861-0.7568-0.55550.2074-0.35-0.3205-0.65280.0979-0.0829-0.05310.5639-0.16210.00041.2649-0.01760.34030.75150.07351.0421448.965-10.894131.925
73.3962-0.0791-2.29530.38610.50961.4654-0.1599-0.2256-0.00660.03060.1633-0.07630.5908-0.21810.00380.7044-0.00820.03041.01810.0341.003424.7937.667136.377
82.6687-0.91190.91530.73360.09661.6371-0.36020.15450.54530.30340.2582-0.03380.05710.10470.00210.9251-0.0291-0.0430.76130.03090.782468.3114.742114.013
93.0403-0.83281.31870.063-0.77590.8457-0.22160.18330.17580.7140.2717-0.1995-0.37770.0052-0.00010.80810.07070.01990.75140.10080.7498467.84918.225110.52
101.3980.74240.31390.68450.31932.08-0.32860.4454-0.0304-0.09320.53210.1746-0.3917-0.6801-0.00390.9907-0.0503-0.00721.19580.26351.0604457.62830.02495.472
110.84120.5443-0.78080.986-0.14990.6876-0.16780.93041.04020.3390.66650.4537-1.0816-0.4253-0.30961.21030.2170.37751.52280.31.3633422.52629.681123.815
121.04370.2797-1.82620.6585-1.82241.29420.48990.58121.26990.36530.39220.7061-0.4137-0.90220.09690.94850.1930.091.10980.29931.4923431.9729.565121.197
130.02210.06190.00110.0127-0.03850.0006-1.08340.0626-0.1010.3737-0.29910.0086-0.8631-0.51050.00140.6515-0.0218-0.36331.0087-0.17650.6992440.6059.27110.478
141.76131.4761-0.02222.23440.26420.76060.08020.049-0.26010.33550.0226-0.00470.0999-0.4283-00.86810.05760.00330.81740.12470.8715447.34617.669118.242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:29 )A3 - 29
2X-RAY DIFFRACTION2( CHAIN A AND RESID 30:63 )A30 - 63
3X-RAY DIFFRACTION3( CHAIN A AND RESID 64:72 )A64 - 72
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:282 )A73 - 282
5X-RAY DIFFRACTION5( CHAIN A AND RESID 283:290 )A283 - 290
6X-RAY DIFFRACTION6( CHAIN A AND RESID 291:392 )A291 - 392
7X-RAY DIFFRACTION7( CHAIN A AND RESID 393:538 )A393 - 538
8X-RAY DIFFRACTION8( CHAIN B AND RESID 5:95 )B5 - 95
9X-RAY DIFFRACTION9( CHAIN B AND RESID 96:159 )B96 - 159
10X-RAY DIFFRACTION10( CHAIN B AND RESID 160:237 )B160 - 237
11X-RAY DIFFRACTION11( CHAIN B AND RESID 238:281 )B238 - 281
12X-RAY DIFFRACTION12( CHAIN B AND RESID 286:356 )B286 - 356
13X-RAY DIFFRACTION13( CHAIN B AND RESID 357:369 )B357 - 369
14X-RAY DIFFRACTION14( CHAIN B AND RESID 370:428 )B370 - 428

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